| title | author | package | output | output_dir | vignette | date | link-citations |
|---|---|---|---|---|---|---|---|
MultiNicheNet analysis: Integrated lung atlas analysis - correct for batch effects to infer differences between IPF and healthy subjects |
Robin Browaeys |
multinichenetr 2.0.1 |
BiocStyle::html_document |
/Users/robinb/Work/multinichenetr/vignettes |
%\VignetteIndexEntry{MultiNicheNet analysis: Integrated lung atlas analysis - correct for batch effects to infer differences between IPF and healthy subjects} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}
|
5 September 2024 |
true |
In this vignette, you can learn how to perform a MultiNicheNet analysis to compare cell-cell communication between two conditions of interest (one-vs-one comparison) while correcting for batch effects. A MultiNicheNet analysis can be performed if you have multi-sample, multi-condition/group single-cell data. We strongly recommend having at least 4 samples in each of the groups/conditions you want to compare. With less samples, the benefits of performing a pseudobulk-based DE analysis are less clear. For those datasets, you can check and run our alternative workflow that makes use of cell-level sample-agnostic differential expression tools.
As input you need a SingleCellExperiment object containing at least the raw count matrix and metadata providing the following information for each cell: the group, sample and cell type.
As example expression data of interacting cells, we will here use merged scRNAseq data from four studies comparing healthy lungs to lungs from patients with idiopathic pulmonary fibrosis (IPF)) (Adams 2020, Reyfman 2019, Morse 2019, and Habermann 2020). Harmonized cell type annotations across the 4 different studies were obtained through Azimuth Azimuth meta-analysis of human scRNA-seq datasets.
We will here demonstrate how MultiNicheNet can exploit the flexibility of generalized linear models in the pseudobulk-edgeR framework to correct for batch effects, here the source study: Adams 2020, Reyfman 2019, Morse 2019, or Habermann 2020. We will apply MultiNicheNet to compare cell-cell interaction changes between IPF and healthy tissue. Note that the only required input for a batch-correcting MultiNicheNet analysis is a merged scRNA-seq object containing raw counts and harmonized cell type annotations.
We will first prepare the MultiNicheNet core analysis, then run the several steps in the MultiNicheNet core analysis, and finally interpret the output.
library(SingleCellExperiment)
library(dplyr)
library(ggplot2)
library(nichenetr)
library(multinichenetr)MultiNicheNet builds upon the NicheNet framework and uses the same prior knowledge networks (ligand-receptor network and ligand-target matrix, currently v2 version).
The Nichenet v2 networks and matrices for both mouse and human can be downloaded from Zenodo 
We will read these object in for human because our expression data is of human patients.
Gene names are here made syntactically valid via make.names() to avoid the loss of genes (eg H2-M3) in downstream visualizations.
organism = "human"options(timeout = 120)
if(organism == "human"){
lr_network_all =
readRDS(url(
"https://zenodo.org/record/10229222/files/lr_network_human_allInfo_30112033.rds"
)) %>%
mutate(
ligand = convert_alias_to_symbols(ligand, organism = organism),
receptor = convert_alias_to_symbols(receptor, organism = organism))
lr_network_all = lr_network_all %>%
mutate(ligand = make.names(ligand), receptor = make.names(receptor))
lr_network = lr_network_all %>%
distinct(ligand, receptor)
ligand_target_matrix = readRDS(url(
"https://zenodo.org/record/7074291/files/ligand_target_matrix_nsga2r_final.rds"
))
colnames(ligand_target_matrix) = colnames(ligand_target_matrix) %>%
convert_alias_to_symbols(organism = organism) %>% make.names()
rownames(ligand_target_matrix) = rownames(ligand_target_matrix) %>%
convert_alias_to_symbols(organism = organism) %>% make.names()
lr_network = lr_network %>% filter(ligand %in% colnames(ligand_target_matrix))
ligand_target_matrix = ligand_target_matrix[, lr_network$ligand %>% unique()]
} else if(organism == "mouse"){
lr_network_all = readRDS(url(
"https://zenodo.org/record/10229222/files/lr_network_mouse_allInfo_30112033.rds"
)) %>%
mutate(
ligand = convert_alias_to_symbols(ligand, organism = organism),
receptor = convert_alias_to_symbols(receptor, organism = organism))
lr_network_all = lr_network_all %>%
mutate(ligand = make.names(ligand), receptor = make.names(receptor))
lr_network = lr_network_all %>%
distinct(ligand, receptor)
ligand_target_matrix = readRDS(url(
"https://zenodo.org/record/7074291/files/ligand_target_matrix_nsga2r_final_mouse.rds"
))
colnames(ligand_target_matrix) = colnames(ligand_target_matrix) %>%
convert_alias_to_symbols(organism = organism) %>% make.names()
rownames(ligand_target_matrix) = rownames(ligand_target_matrix) %>%
convert_alias_to_symbols(organism = organism) %>% make.names()
lr_network = lr_network %>% filter(ligand %in% colnames(ligand_target_matrix))
ligand_target_matrix = ligand_target_matrix[, lr_network$ligand %>% unique()]
}In this vignette, we will load in a subset of the integrated lung atlas data. For the sake of demonstration, this subset only contains 4 cell types.
If you start from a Seurat object, you can convert it easily to a SingleCellExperiment object via sce = Seurat::as.SingleCellExperiment(seurat_obj, assay = "RNA").
Because the NicheNet 2.0. networks are in the most recent version of the official gene symbols, we will make sure that the gene symbols used in the expression data are also updated (= converted from their "aliases" to official gene symbols). Afterwards, we will make them again syntactically valid.
sce = readRDS(url(
"https://zenodo.org/record/8010790/files/sce_subset_lung.rds"
))
sce = alias_to_symbol_SCE(sce, "human") %>% makenames_SCE()In this step, we will formalize our research question into MultiNicheNet input arguments.
In this case study, we want to study differences in cell-cell communication changes between two patient groups (IPF patients vs healthy subjects), while considering the source dataset cells were derived from. Patient groups are indicated in the following meta data column: disease, which has 2 different values: idiopathic.pulmonary.fibrosis and normal.
Cell type annotations are indicated in the annotation.l1 column, and the sample is indicated by the donor column.
If your cells are annotated in multiple hierarchical levels, we recommend using a relatively high level in the hierarchy. This for 2 reasons: 1) MultiNicheNet focuses on differential expression and not differential abundance, and 2) there should be sufficient cells per sample-celltype combination (see later).
sample_id = "donor"
group_id = "disease"
celltype_id = "annotation.l1"Important: It is required that each sample-id is uniquely assigned to only one condition/group of interest. See the vignettes about paired and multifactorial analysis to see how to define your analysis input when you have multiple samples (and conditions) per patient.
If you would have batch effects or covariates you can correct for, you can define this here as well. Here, we want to correct for the source study, which is indicated in the following meta data column: dataset_origin, which has 4 different values: adams_2020, habermann_2020, morse_2019, reyfman_2019 and normal.
covariates = NA
batches = "dataset_origin"Important: for categorical covariates and batches, there should be at least one sample for every group-batch combination. If one of your groups/conditions lacks a certain level of your batch, you won't be able to correct for the batch effect because the model is then not able to distinguish batch from group/condition effects.
Important: The column names of group, sample, cell type, batches and covariates should be syntactically valid (make.names)
Important: All group, sample, cell type, batch and covariate names should be syntactically valid as well (make.names) (eg through SummarizedExperiment::colData(sce)$ShortID = SummarizedExperiment::colData(sce)$ShortID %>% make.names())
For this analysis, we want to compare how cell-cell communication differs between IPF and normal lungs.
contrasts_oi = c("'idiopathic.pulmonary.fibrosis-normal','normal-idiopathic.pulmonary.fibrosis'")Very Important Note the format to indicate the contrasts! This formatting should be adhered to very strictly, and white spaces are not allowed! Check ?get_DE_info for explanation about how to define this well. The most important points are that:
*each contrast is surrounded by single quotation marks
*contrasts are separated by a comma without any white space
*all contrasts together are surrounded by double quotation marks.
If you compare against two groups, you should divide by 2 (as demonstrated in other vignettes), if you compare against three groups, you should divide by 3 and so on.
For downstream visualizations and linking contrasts to their main condition, we also need to run the following: This is necessary because we will also calculate cell-type+condition specificity of ligands and receptors.
contrast_tbl = tibble(contrast =
c("idiopathic.pulmonary.fibrosis-normal", "normal-idiopathic.pulmonary.fibrosis"),
group = c("idiopathic.pulmonary.fibrosis", "normal"))Other vignettes will demonstrate how to formalize different types of research questions.
If you want to focus the analysis on specific cell types (e.g. because you know which cell types reside in the same microenvironments based on spatial data), you can define this here. If you have sufficient computational resources and no specific idea of cell-type colocalzations, we recommend to consider all cell types as potential senders and receivers. Later on during analysis of the output it is still possible to zoom in on the cell types that interest you most, but your analysis is not biased to them.
Here we will consider all cell types in the data:
senders_oi = SummarizedExperiment::colData(sce)[,celltype_id] %>% unique()
receivers_oi = SummarizedExperiment::colData(sce)[,celltype_id] %>% unique()
sce = sce[, SummarizedExperiment::colData(sce)[,celltype_id] %in%
c(senders_oi, receivers_oi)
]In case you would have samples in your data that do not belong to one of the groups/conditions of interest, we recommend removing them and only keeping conditions of interest. This may be especially relevant in atlas settings where you may have cells from patients belonging to diseases that are outside of the scope of the current comparison.
conditions_keep = c("normal", "idiopathic.pulmonary.fibrosis")
sce = sce[, SummarizedExperiment::colData(sce)[,group_id] %in%
conditions_keep
]Now we will run the core of a MultiNicheNet analysis. This analysis consists of the following steps:
-
- Cell-type filtering: determine which cell types are sufficiently present
-
- Gene filtering: determine which genes are sufficiently expressed in each present cell type
-
- Pseudobulk expression calculation: determine and normalize per-sample pseudobulk expression levels for each expressed gene in each present cell type
-
- Differential expression (DE) analysis: determine which genes are differentially expressed
-
- Ligand activity prediction: use the DE analysis output to predict the activity of ligands in receiver cell types and infer their potential target genes
-
- Prioritization: rank cell-cell communication patterns through multi-criteria prioritization
Following these steps, one can optionally
-
- Calculate the across-samples expression correlation between ligand-receptor pairs and target genes
-
- Prioritize communication patterns involving condition-specific cell types through an alternative prioritization scheme
After these steps, the output can be further explored as we will demonstrate in the "Downstream analysis of the MultiNicheNet output" section.
In this vignette, we will demonstrate these steps one-by-one, which offers the most flexibility to the user to assess intermediary results. Other vignettes will demonstrate the use of the multi_nichenet_analysis wrapper function.
In this step we will calculate and visualize cell type abundances. This will give an indication about which cell types will be retained in the analysis, and which cell types will be filtered out.
Since MultiNicheNet will infer group differences at the sample level for each cell type (currently via Muscat - pseudobulking + EdgeR), we need to have sufficient cells per sample of a cell type, and this for all groups. In the following analysis we will set this minimum number of cells per cell type per sample at 10. Samples that have less than min_cells cells will be excluded from the analysis for that specific cell type.
min_cells = 10We recommend using min_cells = 10, except for datasets with several lowly abundant cell types of interest. For those datasets, we recommend using min_cells = 5.
abundance_info = get_abundance_info(
sce = sce,
sample_id = sample_id, group_id = group_id, celltype_id = celltype_id,
min_cells = min_cells,
senders_oi = senders_oi, receivers_oi = receivers_oi,
batches = batches
)First, we will check the cell type abundance diagnostic plots.
The first plot visualizes the number of cells per celltype-sample combination, and indicates which combinations are removed during the DE analysis because there are less than min_cells in the celltype-sample combination.
abundance_info$abund_plot_sample
The red dotted line indicates the required minimum of cells as defined above in min_cells. We can see here that some sample-celltype combinations are left out. For the DE analysis in the next step, only cell types will be considered if there are at least two samples per condition-batch combination with a sufficient number of cells.
Important: Based on the cell type abundance diagnostics, we recommend users to change their analysis settings if required (eg changing cell type annotation level, batches, ...), before proceeding with the rest of the analysis. If too many celltype-sample combinations don't pass this threshold, we recommend to define your cell types in a more general way (use one level higher of the cell type ontology hierarchy) (eg TH17 CD4T cells --> CD4T cells) or use min_cells = 5 if this would not be possible.
Running the following block of code can help you determine which cell types are condition-specific and which cell types are absent.
abundance_df_summarized = abundance_info$abundance_data %>%
mutate(keep = as.logical(keep)) %>%
group_by(group_id, celltype_id) %>%
summarise(samples_present = sum((keep)))
celltypes_absent_one_condition = abundance_df_summarized %>%
filter(samples_present == 0) %>% pull(celltype_id) %>% unique()
# find truly condition-specific cell types by searching for cell types
# truely absent in at least one condition
celltypes_present_one_condition = abundance_df_summarized %>%
filter(samples_present >= 2) %>% pull(celltype_id) %>% unique()
# require presence in at least 2 samples of one group so
# it is really present in at least one condition
condition_specific_celltypes = intersect(
celltypes_absent_one_condition,
celltypes_present_one_condition)
total_nr_conditions = SummarizedExperiment::colData(sce)[,group_id] %>%
unique() %>% length()
absent_celltypes = abundance_df_summarized %>%
filter(samples_present < 2) %>%
group_by(celltype_id) %>%
count() %>%
filter(n == total_nr_conditions) %>%
pull(celltype_id)
print("condition-specific celltypes:")
## [1] "condition-specific celltypes:"
print(condition_specific_celltypes)
## character(0)
print("absent celltypes:")
## [1] "absent celltypes:"
print(absent_celltypes)
## character(0)Absent cell types will be filtered out, condition-specific cell types can be filtered out if you as a user do not want to run the alternative workflow for condition-specific cell types in the optional step 8 of the core MultiNicheNet analysis.
analyse_condition_specific_celltypes = FALSEif(analyse_condition_specific_celltypes == TRUE){
senders_oi = senders_oi %>% setdiff(absent_celltypes)
receivers_oi = receivers_oi %>% setdiff(absent_celltypes)
} else {
senders_oi = senders_oi %>%
setdiff(union(absent_celltypes, condition_specific_celltypes))
receivers_oi = receivers_oi %>%
setdiff(union(absent_celltypes, condition_specific_celltypes))
}
sce = sce[, SummarizedExperiment::colData(sce)[,celltype_id] %in%
c(senders_oi, receivers_oi)
]Before running the DE analysis, we will determine which genes are not sufficiently expressed and should be filtered out.
We will perform gene filtering based on a similar procedure as used in edgeR::filterByExpr. However, we adapted this procedure to be more interpretable for single-cell datasets.
For each cell type, we will consider genes expressed if they are expressed in at least a min_sample_prop fraction of samples in the condition with the lowest number of samples. By default, we set min_sample_prop = 0.50, which means that genes should be expressed in at least 2 samples if the group with lowest nr. of samples has 4 samples like this dataset.
min_sample_prop = 0.50But how do we define which genes are expressed in a sample? For this we will consider genes as expressed if they have non-zero expression values in a fraction_cutoff fraction of cells of that cell type in that sample. By default, we set fraction_cutoff = 0.05, which means that genes should show non-zero expression values in at least 5% of cells in a sample.
fraction_cutoff = 0.05We recommend using these default values unless there is specific interest in prioritizing (very) weakly expressed interactions. In that case, you could lower the value of fraction_cutoff. We explicitly recommend against using fraction_cutoff > 0.10.
Now we will calculate the information required for gene filtering with the following command:
frq_list = get_frac_exprs(
sce = sce,
sample_id = sample_id, celltype_id = celltype_id, group_id = group_id,
batches = batches,
min_cells = min_cells,
fraction_cutoff = fraction_cutoff, min_sample_prop = min_sample_prop)
## [1] "Samples are considered if they have more than 10 cells of the cell type of interest"
## [1] "Genes with non-zero counts in at least 5% of cells of a cell type of interest in a particular sample will be considered as expressed in that sample."
## [1] "Genes expressed in at least 6 samples will considered as expressed in the cell type: Alveolar.Epithelial.Type.1"
## [1] "Genes expressed in at least 16 samples will considered as expressed in the cell type: CD16..Monocyte"
## [1] "Genes expressed in at least 16 samples will considered as expressed in the cell type: Fibroblast"
## [1] "Genes expressed in at least 6.5 samples will considered as expressed in the cell type: Proliferating.Macrophage"
## [1] "10193 genes are considered as expressed in the cell type: Alveolar.Epithelial.Type.1"
## [1] "8810 genes are considered as expressed in the cell type: CD16..Monocyte"
## [1] "10643 genes are considered as expressed in the cell type: Fibroblast"
## [1] "11018 genes are considered as expressed in the cell type: Proliferating.Macrophage"Now only keep genes that are expressed by at least one cell type:
genes_oi = frq_list$expressed_df %>%
filter(expressed == TRUE) %>% pull(gene) %>% unique()
sce = sce[genes_oi, ]Pseudobulk expression calculation: determine and normalize per-sample pseudobulk expression levels for each expressed gene in each present cell type
After filtering out absent cell types and genes, we will continue the analysis by calculating the different prioritization criteria that we will use to prioritize cell-cell communication patterns.
First, we will determine and normalize per-sample pseudobulk expression levels for each expressed gene in each present cell type. The function process_abundance_expression_info will link this expression information for ligands of the sender cell types to the corresponding receptors of the receiver cell types. This will later on allow us to define the cell-type specicificy criteria for ligands and receptors.
abundance_expression_info = process_abundance_expression_info(
sce = sce,
sample_id = sample_id, group_id = group_id, celltype_id = celltype_id,
min_cells = min_cells,
senders_oi = senders_oi, receivers_oi = receivers_oi,
lr_network = lr_network,
batches = batches,
frq_list = frq_list,
abundance_info = abundance_info)Normalized pseudobulk expression values per gene/celltype/sample can be inspected by:
abundance_expression_info$celltype_info$pb_df %>% head()
## # A tibble: 6 × 4
## gene sample pb_sample celltype
## <chr> <chr> <dbl> <fct>
## 1 A1BG pVUHD66 6.07 CD16..Monocyte
## 2 A2M pVUHD66 4.53 CD16..Monocyte
## 3 A2ML1 pVUHD66 0 CD16..Monocyte
## 4 A3GALT2 pVUHD66 0 CD16..Monocyte
## 5 A4GALT pVUHD66 0 CD16..Monocyte
## 6 A4GNT pVUHD66 0 CD16..MonocyteAn average of these sample-level expression values per condition/group can be inspected by:
abundance_expression_info$celltype_info$pb_df_group %>% head()
## # A tibble: 6 × 4
## # Groups: group, celltype [1]
## group celltype gene pb_group
## <chr> <chr> <chr> <dbl>
## 1 idiopathic.pulmonary.fibrosis Alveolar.Epithelial.Type.1 A1BG 3.37
## 2 idiopathic.pulmonary.fibrosis Alveolar.Epithelial.Type.1 A2M 2.73
## 3 idiopathic.pulmonary.fibrosis Alveolar.Epithelial.Type.1 A2ML1 0.410
## 4 idiopathic.pulmonary.fibrosis Alveolar.Epithelial.Type.1 A3GALT2 0
## 5 idiopathic.pulmonary.fibrosis Alveolar.Epithelial.Type.1 A4GALT 1.07
## 6 idiopathic.pulmonary.fibrosis Alveolar.Epithelial.Type.1 A4GNT 0Inspecting these values for ligand-receptor interactions can be done by:
abundance_expression_info$sender_receiver_info$pb_df %>% head()
## # A tibble: 6 × 8
## sample sender receiver ligand receptor pb_ligand pb_receptor ligand_receptor_pb_prod
## <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
## 1 pTILD006 Fibroblast Fibroblast TIMP1 CD63 14.4 12.6 182.
## 2 pTILD006 CD16..Monocyte Fibroblast TIMP1 CD63 13.7 12.6 174.
## 3 p208C Fibroblast Fibroblast TIMP1 CD63 15.0 11.5 173.
## 4 pDonor_07 Fibroblast Alveolar.Epithelial.Type.1 TIMP1 CD63 14.4 12.0 173.
## 5 pDonor_07 Fibroblast Fibroblast TIMP1 CD63 14.4 11.7 169.
## 6 pTILD006 Fibroblast CD16..Monocyte TIMP1 CD63 14.4 11.6 167.
abundance_expression_info$sender_receiver_info$pb_df_group %>% head()
## # A tibble: 6 × 8
## # Groups: group, sender [2]
## group sender receiver ligand receptor pb_ligand_group pb_receptor_group ligand_receptor_pb_prod_group
## <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
## 1 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast TIMP1 CD63 12.5 11.3 142.
## 2 idiopathic.pulmonary.fibrosis Fibroblast Proliferating.Macrophage TIMP1 CD63 12.5 11.2 140.
## 3 normal Fibroblast Fibroblast TIMP1 CD63 12.5 10.9 137.
## 4 idiopathic.pulmonary.fibrosis Fibroblast Alveolar.Epithelial.Type.1 TIMP1 CD63 12.5 10.9 136.
## 5 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast TIMP1 MMP2 12.5 10.7 134.
## 6 normal Fibroblast Alveolar.Epithelial.Type.1 TIMP1 CD63 12.5 10.7 134.In this step, we will perform genome-wide differential expression analysis of receiver and sender cell types to define DE genes between the conditions of interest (as formalized by the contrasts_oi). Based on this analysis, we later can define the levels of differential expression of ligands in senders and receptors in receivers, and define the set of affected target genes in the receiver cell types (which will be used for the ligand activity analysis).
We will apply pseudobulking followed by EdgeR to perform multi-condition multi-sample differential expression (DE) analysis (also called 'differential state' analysis by the developers of Muscat).
DE_info = get_DE_info(
sce = sce,
sample_id = sample_id, group_id = group_id, celltype_id = celltype_id,
batches = batches, covariates = covariates,
contrasts_oi = contrasts_oi,
min_cells = min_cells,
expressed_df = frq_list$expressed_df)
## [1] "DE analysis is done:"
## [1] "included cell types are:"
## [1] "CD16..Monocyte" "Alveolar.Epithelial.Type.1" "Fibroblast" "Proliferating.Macrophage"Check DE output information in table with logFC and p-values for each gene-celltype-contrast:
DE_info$celltype_de$de_output_tidy %>% head()
## # A tibble: 6 × 9
## gene cluster_id logFC logCPM F p_val p_adj.loc p_adj contrast
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <chr>
## 1 A1BG CD16..Monocyte -0.143 5.07 0.337 0.563 0.827 0.827 idiopathic.pulmonary.fibrosis-normal
## 2 A2M CD16..Monocyte 0.514 4.04 2.61 0.109 0.366 0.366 idiopathic.pulmonary.fibrosis-normal
## 3 AAAS CD16..Monocyte 0.0185 4.46 0.00473 0.945 0.987 0.987 idiopathic.pulmonary.fibrosis-normal
## 4 AACS CD16..Monocyte -0.59 3.89 2.94 0.09 0.334 0.334 idiopathic.pulmonary.fibrosis-normal
## 5 AAGAB CD16..Monocyte -0.137 5.47 0.594 0.443 0.743 0.743 idiopathic.pulmonary.fibrosis-normal
## 6 AAK1 CD16..Monocyte -0.352 6.7 5.96 0.0166 0.123 0.123 idiopathic.pulmonary.fibrosis-normalEvaluate the distributions of p-values:
DE_info$hist_pvals
These distributions look fine (uniform distribution, except peak at p-value <= 0.05), so we will continue using these regular p-values. In case these p-value distributions look irregular, you can estimate empirical p-values as we will demonstrate in another vignette.
empirical_pval = FALSEif(empirical_pval == TRUE){
DE_info_emp = get_empirical_pvals(DE_info$celltype_de$de_output_tidy)
celltype_de = DE_info_emp$de_output_tidy_emp %>% select(-p_val, -p_adj) %>%
rename(p_val = p_emp, p_adj = p_adj_emp)
} else {
celltype_de = DE_info$celltype_de$de_output_tidy
} To end this step, we will combine the DE information of senders and receivers by linking their ligands and receptors together based on the prior knowledge ligand-receptor network.
sender_receiver_de = combine_sender_receiver_de(
sender_de = celltype_de,
receiver_de = celltype_de,
senders_oi = senders_oi,
receivers_oi = receivers_oi,
lr_network = lr_network
)sender_receiver_de %>% head(20)
## # A tibble: 20 × 12
## contrast sender receiver ligand receptor lfc_ligand lfc_receptor ligand_receptor_lfc_avg p_val_ligand p_adj_ligand p_val_receptor p_adj_receptor
## <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 idiopathic.pulmonary.fibrosis-normal Alveolar.Epithelial.Type.1 Alveolar.Epithelial.Type.1 CDH2 CDH2 4.05 4.05 4.05 2.21e-10 9.40e- 8 2.21e-10 0.000000094
## 2 idiopathic.pulmonary.fibrosis-normal Alveolar.Epithelial.Type.1 Proliferating.Macrophage AREG MMP9 2.94 3.86 3.4 1.22e- 7 2.64e- 5 3.76e- 5 0.00345
## 3 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Proliferating.Macrophage PPBP GRM7 5.42 1.21 3.32 2.43e- 8 2.43e- 5 1.05e- 2 0.112
## 4 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Fibroblast SPP1 ITGA8 5.01 1.51 3.26 1.24e- 6 3.58e- 4 6.5 e- 5 0.00239
## 5 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Alveolar.Epithelial.Type.1 SPP1 ITGB6 5.01 1.44 3.22 1.24e- 6 3.58e- 4 2.44e- 9 0.000000804
## 6 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Fibroblast PPBP ADRA2A 5.42 0.968 3.19 2.43e- 8 2.43e- 5 2.21e- 2 0.132
## 7 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Alveolar.Epithelial.Type.1 SPP1 ITGAV 5.01 1.31 3.16 1.24e- 6 3.58e- 4 6.28e- 7 0.000108
## 8 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Proliferating.Macrophage PPBP OPRD1 5.42 0.817 3.12 2.43e- 8 2.43e- 5 2.68e- 1 0.608
## 9 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Proliferating.Macrophage CCL7 CCR3 4.92 1.25 3.08 1.15e- 8 2.14e- 5 4.15e- 2 0.237
## 10 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Proliferating.Macrophage SPP1 ITGA8 5.01 1.07 3.04 1.24e- 6 3.58e- 4 1.07e- 1 0.394
## 11 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Proliferating.Macrophage CCL22 DPP4 3.27 2.78 3.02 3.05e- 3 5.32e- 2 4.44e- 3 0.0662
## 12 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Fibroblast PPBP OPRM1 5.42 0.592 3.01 2.43e- 8 2.43e- 5 1.99e- 1 0.486
## 13 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Proliferating.Macrophage TIMP3 MMP9 2.03 3.86 2.94 1.37e- 3 3.37e- 2 3.76e- 5 0.00345
## 14 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Fibroblast PPBP GRM7 5.42 0.353 2.89 2.43e- 8 2.43e- 5 2.37e- 1 0.532
## 15 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Alveolar.Epithelial.Type.1 SPP1 ITGB5 5.01 0.714 2.86 1.24e- 6 3.58e- 4 2.67e- 2 0.275
## 16 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Proliferating.Macrophage CCL7 CCR5 4.92 0.801 2.86 1.15e- 8 2.14e- 5 9.49e- 2 0.371
## 17 normal-idiopathic.pulmonary.fibrosis Fibroblast Alveolar.Epithelial.Type.1 HP APOA1 2.61 3.06 2.84 5.18e- 5 2.03e- 3 6.25e- 5 0.00472
## 18 idiopathic.pulmonary.fibrosis-normal Alveolar.Epithelial.Type.1 Alveolar.Epithelial.Type.1 MMP7 ERBB4 4.48 1.15 2.82 1.75e-13 2.54e-10 1.03e- 2 0.158
## 19 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Proliferating.Macrophage SPP1 ITGA9 5.01 0.598 2.80 1.24e- 6 3.58e- 4 2.13e- 1 0.546
## 20 idiopathic.pulmonary.fibrosis-normal Proliferating.Macrophage Alveolar.Epithelial.Type.1 PPBP GRM7 5.42 0.177 2.80 2.43e- 8 2.43e- 5 7.77e- 1 0.961Ligand activity prediction: use the DE analysis output to predict the activity of ligands in receiver cell types and infer their potential target genes
In this step, we will predict NicheNet ligand activities and NicheNet ligand-target links based on these differential expression results. We do this to prioritize interactions based on their predicted effect on a receiver cell type. We will assume that the most important group-specific interactions are those that lead to group-specific gene expression changes in a receiver cell type.
Similarly to base NicheNet (https://github.com/saeyslab/nichenetr), we use the DE output to create a "geneset of interest": here we assume that DE genes within a cell type may be DE because of differential cell-cell communication processes. In the ligand activity prediction, we will assess the enrichment of target genes of ligands within this geneset of interest. In case high-probabiliy target genes of a ligand are enriched in this set compared to the background of expressed genes, we predict that this ligand may have a high activity.
Because the ligand activity analysis is an enrichment procedure, it is important that this geneset of interest should contain a sufficient but not too large number of genes. The ratio geneset_oi/background should ideally be between 1/200 and 1/10 (or close to these ratios).
To determine the genesets of interest based on DE output, we need to define some logFC and/or p-value thresholds per cell type/contrast combination. In general, we recommend inspecting the nr. of DE genes for all cell types based on the default thresholds and adapting accordingly. By default, we will apply the p-value cutoff on the normal p-values, and not on the p-values corrected for multiple testing. This choice was made because most multi-sample single-cell transcriptomics datasets have just a few samples per group and we might have a lack of statistical power due to pseudobulking. But, if the smallest group >= 20 samples, we typically recommend using p_val_adj = TRUE. When the biological difference between the conditions is very large, we typically recommend increasing the logFC_threshold and/or using p_val_adj = TRUE.
Assess geneset_oi-vs-background ratios for different DE output tresholds prior to the NicheNet ligand activity analysis
Because we have data with many samples here, we will first inspect the geneset_oi-vs-background ratios in case of using the adjusted p-values:
logFC_threshold = 0.50
p_val_threshold = 0.05p_val_adj = TRUE geneset_assessment = contrast_tbl$contrast %>%
lapply(
process_geneset_data,
celltype_de, logFC_threshold, p_val_adj, p_val_threshold
) %>%
bind_rows()
geneset_assessment
## # A tibble: 8 × 12
## cluster_id n_background n_geneset_up n_geneset_down prop_geneset_up prop_geneset_down in_range_up in_range_down contrast logFC_threshold p_val_threshold adjusted
## <chr> <int> <int> <int> <dbl> <dbl> <lgl> <lgl> <chr> <dbl> <dbl> <lgl>
## 1 Alveolar.Epithelial.Type.1 10193 227 91 0.0223 0.00893 TRUE TRUE idiopathic.pulmonary.fibrosis-normal 0.5 0.05 TRUE
## 2 CD16..Monocyte 8810 249 366 0.0283 0.0415 TRUE TRUE idiopathic.pulmonary.fibrosis-normal 0.5 0.05 TRUE
## 3 Fibroblast 10643 658 302 0.0618 0.0284 TRUE TRUE idiopathic.pulmonary.fibrosis-normal 0.5 0.05 TRUE
## 4 Proliferating.Macrophage 11018 259 270 0.0235 0.0245 TRUE TRUE idiopathic.pulmonary.fibrosis-normal 0.5 0.05 TRUE
## 5 Alveolar.Epithelial.Type.1 10193 91 227 0.00893 0.0223 TRUE TRUE normal-idiopathic.pulmonary.fibrosis 0.5 0.05 TRUE
## 6 CD16..Monocyte 8810 366 249 0.0415 0.0283 TRUE TRUE normal-idiopathic.pulmonary.fibrosis 0.5 0.05 TRUE
## 7 Fibroblast 10643 302 658 0.0284 0.0618 TRUE TRUE normal-idiopathic.pulmonary.fibrosis 0.5 0.05 TRUE
## 8 Proliferating.Macrophage 11018 270 259 0.0245 0.0235 TRUE TRUE normal-idiopathic.pulmonary.fibrosis 0.5 0.05 TRUEWe can see here that for all cell type / contrast combinations, all geneset/background ratio's are within the recommended range (in_range_up and in_range_down columns), and we will therefore proceed with these tresholds for the ligand activity analysis. When these geneset/background ratio's would not be within the recommended ranges, we should interpret ligand activity results for these cell types with more caution, or use different thresholds (for these or all cell types).
After the ligand activity prediction, we will also infer the predicted target genes of these ligands in each contrast. For this ligand-target inference procedure, we also need to select which top n of the predicted target genes will be considered (here: top 250 targets per ligand). This parameter will not affect the ligand activity predictions. It will only affect ligand-target visualizations and construction of the intercellular regulatory network during the downstream analysis. We recommend users to test other settings in case they would be interested in exploring fewer, but more confident target genes, or vice versa.
top_n_target = 250The NicheNet ligand activity analysis can be run in parallel for each receiver cell type, by changing the number of cores as defined here. Using more cores will speed up the analysis at the cost of needing more memory. This is only recommended if you have many receiver cell types of interest.
verbose = TRUE
cores_system = 8
n.cores = min(cores_system, celltype_de$cluster_id %>% unique() %>% length()) Running the ligand activity prediction will take some time (the more cell types and contrasts, the more time)
ligand_activities_targets_DEgenes = suppressMessages(suppressWarnings(
get_ligand_activities_targets_DEgenes(
receiver_de = celltype_de,
receivers_oi = intersect(receivers_oi, celltype_de$cluster_id %>% unique()),
ligand_target_matrix = ligand_target_matrix,
logFC_threshold = logFC_threshold,
p_val_threshold = p_val_threshold,
p_val_adj = p_val_adj,
top_n_target = top_n_target,
verbose = verbose,
n.cores = n.cores
)
))You can check the output of the ligand activity and ligand-target inference here:
ligand_activities_targets_DEgenes$ligand_activities %>% head(20)
## # A tibble: 20 × 8
## # Groups: receiver, contrast [1]
## ligand activity contrast target ligand_target_weight receiver direction_regulation activity_scaled
## <chr> <dbl> <chr> <chr> <dbl> <chr> <fct> <dbl>
## 1 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal BAX 0.0115 Alveolar.Epithelial.Type.1 up 0.469
## 2 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal BMP4 0.00776 Alveolar.Epithelial.Type.1 up 0.469
## 3 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal CCL2 0.0117 Alveolar.Epithelial.Type.1 up 0.469
## 4 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal CCND1 0.0186 Alveolar.Epithelial.Type.1 up 0.469
## 5 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal CCND2 0.00954 Alveolar.Epithelial.Type.1 up 0.469
## 6 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal CDKN2A 0.00716 Alveolar.Epithelial.Type.1 up 0.469
## 7 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal COL1A1 0.00720 Alveolar.Epithelial.Type.1 up 0.469
## 8 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal COL1A2 0.00834 Alveolar.Epithelial.Type.1 up 0.469
## 9 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal CTNNB1 0.00691 Alveolar.Epithelial.Type.1 up 0.469
## 10 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal DUSP6 0.00908 Alveolar.Epithelial.Type.1 up 0.469
## 11 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal E2F3 0.00678 Alveolar.Epithelial.Type.1 up 0.469
## 12 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal FN1 0.00965 Alveolar.Epithelial.Type.1 up 0.469
## 13 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal IFI16 0.00727 Alveolar.Epithelial.Type.1 up 0.469
## 14 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal NFIA 0.00700 Alveolar.Epithelial.Type.1 up 0.469
## 15 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal PCDH7 0.00677 Alveolar.Epithelial.Type.1 up 0.469
## 16 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal PHLDA1 0.00690 Alveolar.Epithelial.Type.1 up 0.469
## 17 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal PLAU 0.00999 Alveolar.Epithelial.Type.1 up 0.469
## 18 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal SERPINE1 0.0140 Alveolar.Epithelial.Type.1 up 0.469
## 19 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal SOCS2 0.00894 Alveolar.Epithelial.Type.1 up 0.469
## 20 A2M 0.0286 idiopathic.pulmonary.fibrosis-normal SOX9 0.00692 Alveolar.Epithelial.Type.1 up 0.469In the previous steps, we calculated expression, differential expression and NicheNet ligand activity. In the final step, we will now combine all calculated information to rank all sender-ligand---receiver-receptor pairs according to group/condition specificity. We will use the following criteria to prioritize ligand-receptor interactions:
- Upregulation of the ligand in a sender cell type and/or upregulation of the receptor in a receiver cell type - in the condition of interest.
- Cell-type specific expression of the ligand in the sender cell type and receptor in the receiver cell type in the condition of interest (to mitigate the influence of upregulated but still relatively weakly expressed ligands/receptors).
- Sufficiently high expression levels of ligand and receptor in many samples of the same group.
- High NicheNet ligand activity, to further prioritize ligand-receptor pairs based on their predicted effect of the ligand-receptor interaction on the gene expression in the receiver cell type.
We will combine these prioritization criteria in a single aggregated prioritization score. In the default setting, we will weigh each of these criteria equally (scenario = "regular"). This setting is strongly recommended. However, we also provide some additional setting to accomodate different biological scenarios. The setting scenario = "lower_DE" halves the weight for DE criteria and doubles the weight for ligand activity. This is recommended in case your hypothesis is that the differential CCC patterns in your data are less likely to be driven by DE (eg in cases of differential migration into a niche). The setting scenario = "no_frac_LR_expr" ignores the criterion "Sufficiently high expression levels of ligand and receptor in many samples of the same group". This may be interesting for users that have data with a limited number of samples and don’t want to penalize interactions if they are not sufficiently expressed in some samples.
Finally, we still need to make one choice. For NicheNet ligand activity we can choose to prioritize ligands that only induce upregulation of target genes (ligand_activity_down = FALSE) or can lead potentially lead to both up- and downregulation (ligand_activity_down = TRUE). The benefit of ligand_activity_down = FALSE is ease of interpretability: prioritized ligand-receptor pairs will be upregulated in the condition of interest, just like their target genes. ligand_activity_down = TRUE can be harder to interpret because target genes of some interactions may be upregulated in the other conditions compared to the condition of interest. This is harder to interpret, but may help to pick up interactions that can also repress gene expression.
Here we will choose for setting ligand_activity_down = FALSE and focus specifically on upregulating ligands.
ligand_activity_down = FALSEsender_receiver_tbl = sender_receiver_de %>% distinct(sender, receiver)
metadata_combined = SummarizedExperiment::colData(sce) %>% tibble::as_tibble()
if(!is.na(batches)){
grouping_tbl = metadata_combined[,c(sample_id, group_id, batches)] %>%
tibble::as_tibble() %>% distinct()
colnames(grouping_tbl) = c("sample","group",batches)
} else {
grouping_tbl = metadata_combined[,c(sample_id, group_id)] %>%
tibble::as_tibble() %>% distinct()
colnames(grouping_tbl) = c("sample","group")
}
prioritization_tables = suppressMessages(generate_prioritization_tables(
sender_receiver_info = abundance_expression_info$sender_receiver_info,
sender_receiver_de = sender_receiver_de,
ligand_activities_targets_DEgenes = ligand_activities_targets_DEgenes,
contrast_tbl = contrast_tbl,
sender_receiver_tbl = sender_receiver_tbl,
grouping_tbl = grouping_tbl,
scenario = "regular", # all prioritization criteria will be weighted equally
fraction_cutoff = fraction_cutoff,
abundance_data_receiver = abundance_expression_info$abundance_data_receiver,
abundance_data_sender = abundance_expression_info$abundance_data_sender,
ligand_activity_down = ligand_activity_down
))Check the output tables
First: group-based summary table
prioritization_tables$group_prioritization_tbl %>% head(20)
## # A tibble: 20 × 18
## contrast group sender receiver ligand receptor lr_interaction id scaled_lfc_ligand scaled_p_val_ligand_…¹ scaled_lfc_receptor scaled_p_val_recepto…² max_scaled_activity scaled_pb_ligand scaled_pb_receptor fraction_expressing_…³ prioritization_score top_group
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <chr>
## 1 idiopathic.pulmonary.fibrosi… idio… Fibro… Fibrobl… ITM2B ROR2 ITM2B_ROR2 ITM2… 0.771 0.947 0.834 0.938 0.802 1.00 1.00 0.922 0.912 idiopath…
## 2 normal-idiopathic.pulmonary.… norm… CD16.… CD16..M… IL10 IL10RA IL10_IL10RA IL10… 0.947 0.978 0.732 0.912 1.00 1.00 1.00 0.673 0.910 normal
## 3 idiopathic.pulmonary.fibrosi… idio… Fibro… CD16..M… TGM2 ITGA4 TGM2_ITGA4 TGM2… 0.843 0.927 0.839 0.950 0.861 1.00 1.00 0.804 0.908 idiopath…
## 4 idiopathic.pulmonary.fibrosi… idio… Fibro… CD16..M… CXCL14 CXCR4 CXCL14_CXCR4 CXCL… 0.981 0.993 0.911 0.980 0.648 1.00 1.00 0.863 0.908 idiopath…
## 5 idiopathic.pulmonary.fibrosi… idio… Fibro… Prolife… COL14… CD44 COL14A1_CD44 COL1… 0.952 0.992 0.775 0.941 0.708 1.00 1.00 0.902 0.907 idiopath…
## 6 idiopathic.pulmonary.fibrosi… idio… Fibro… CD16..M… CXCL12 CXCR4 CXCL12_CXCR4 CXCL… 0.973 0.998 0.911 0.980 0.642 1.00 1.00 0.863 0.906 idiopath…
## 7 idiopathic.pulmonary.fibrosi… idio… Fibro… Fibrobl… BMP4 ACVR1 BMP4_ACVR1 BMP4… 0.913 0.974 0.709 0.836 1.00 1.00 1.00 0.706 0.904 idiopath…
## 8 idiopathic.pulmonary.fibrosi… idio… Fibro… Fibrobl… A2M MMP2 A2M_MMP2 A2M_… 0.939 0.976 0.887 0.985 0.581 1.00 1.00 0.941 0.903 idiopath…
## 9 idiopathic.pulmonary.fibrosi… idio… Proli… Alveola… FN1 ITGB6 FN1_ITGB6 FN1_… 0.957 0.986 0.974 0.998 0.745 1.00 1.00 0.706 0.902 idiopath…
## 10 idiopathic.pulmonary.fibrosi… idio… Fibro… Fibrobl… SLIT3 ROBO2 SLIT3_ROBO2 SLIT… 0.889 0.981 0.972 0.991 0.627 1.00 1.00 0.843 0.898 idiopath…
## 11 idiopathic.pulmonary.fibrosi… idio… Fibro… Fibrobl… SLIT3 ROBO1 SLIT3_ROBO1 SLIT… 0.889 0.981 0.931 0.992 0.627 1.00 1.00 0.863 0.898 idiopath…
## 12 idiopathic.pulmonary.fibrosi… idio… Proli… Prolife… SPP1 CD44 SPP1_CD44 SPP1… 1.00 0.979 0.775 0.941 0.601 1.00 1.00 0.922 0.895 idiopath…
## 13 idiopathic.pulmonary.fibrosi… idio… Fibro… Fibrobl… COL6A3 ITGA1 COL6A3_ITGA1 COL6… 0.836 0.956 0.819 0.903 0.747 1.00 1.00 0.863 0.895 idiopath…
## 14 idiopathic.pulmonary.fibrosi… idio… Proli… Prolife… FN1 SDC2 FN1_SDC2 FN1_… 0.957 0.986 0.874 0.909 0.573 1.00 1.00 0.922 0.893 idiopath…
## 15 idiopathic.pulmonary.fibrosi… idio… Fibro… CD16..M… MDK ITGA4 MDK_ITGA4 MDK_… 0.877 0.901 0.839 0.950 0.750 1.00 1.00 0.824 0.893 idiopath…
## 16 idiopathic.pulmonary.fibrosi… idio… Proli… Fibrobl… FN1 ITGA8 FN1_ITGA8 FN1_… 0.957 0.986 0.979 0.979 0.622 1.00 1.00 0.784 0.893 idiopath…
## 17 idiopathic.pulmonary.fibrosi… idio… Fibro… Fibrobl… COL5A1 ITGA1 COL5A1_ITGA1 COL5… 0.676 0.765 0.819 0.903 0.912 1.00 1.00 0.863 0.893 idiopath…
## 18 idiopathic.pulmonary.fibrosi… idio… Fibro… Fibrobl… COL5A1 SDC3 COL5A1_SDC3 COL5… 0.676 0.765 0.965 0.990 0.912 1.00 1.00 0.745 0.893 idiopath…
## 19 idiopathic.pulmonary.fibrosi… idio… Fibro… Alveola… FN1 ITGB6 FN1_ITGB6 FN1_… 0.846 0.945 0.974 0.998 0.745 0.983 1.00 0.745 0.893 idiopath…
## 20 idiopathic.pulmonary.fibrosi… idio… Fibro… Prolife… CFH ITGAM CFH_ITGAM CFH_… 0.919 0.989 0.949 0.994 0.543 1.00 1.00 0.882 0.892 idiopath…
## # ℹ abbreviated names: ¹scaled_p_val_ligand_adapted, ²scaled_p_val_receptor_adapted, ³fraction_expressing_ligand_receptorThis table gives the final prioritization score of each interaction, and the values of the individual prioritization criteria.
With this step, all required steps are finished. Now, we can optionally still run the following steps
- Calculate the across-samples expression correlation between ligand-receptor pairs and target genes
- Prioritize communication patterns involving condition-specific cell types through an alternative prioritization scheme
Here we will only focus on the expression correlation step:
In multi-sample datasets, we have the opportunity to look whether expression of ligand-receptor across all samples is correlated with the expression of their by NicheNet predicted target genes. This is what we will do with the following line of code:
lr_target_prior_cor = lr_target_prior_cor_inference(
receivers_oi = prioritization_tables$group_prioritization_tbl$receiver %>% unique(),
abundance_expression_info = abundance_expression_info,
celltype_de = celltype_de,
grouping_tbl = grouping_tbl,
prioritization_tables = prioritization_tables,
ligand_target_matrix = ligand_target_matrix,
logFC_threshold = logFC_threshold,
p_val_threshold = p_val_threshold,
p_val_adj = p_val_adj
)To avoid needing to redo the analysis later, we will here to save an output object that contains all information to perform all downstream analyses.
path = "./"
multinichenet_output = list(
celltype_info = abundance_expression_info$celltype_info,
celltype_de = celltype_de,
sender_receiver_info = abundance_expression_info$sender_receiver_info,
sender_receiver_de = sender_receiver_de,
ligand_activities_targets_DEgenes = ligand_activities_targets_DEgenes,
prioritization_tables = prioritization_tables,
grouping_tbl = grouping_tbl,
lr_target_prior_cor = lr_target_prior_cor
)
multinichenet_output = make_lite_output(multinichenet_output)
save = FALSE
if(save == TRUE){
saveRDS(multinichenet_output, paste0(path, "multinichenet_output.rds"))
}In a first instance, we will look at the broad overview of prioritized interactions via condition-specific Chordiagram circos plots.
We will look here at the top 50 predictions across all contrasts, senders, and receivers of interest.
prioritized_tbl_oi_all = get_top_n_lr_pairs(
multinichenet_output$prioritization_tables,
top_n = 50,
rank_per_group = FALSE
)prioritized_tbl_oi =
multinichenet_output$prioritization_tables$group_prioritization_tbl %>%
filter(id %in% prioritized_tbl_oi_all$id) %>%
distinct(id, sender, receiver, ligand, receptor, group) %>%
left_join(prioritized_tbl_oi_all)
prioritized_tbl_oi$prioritization_score[is.na(prioritized_tbl_oi$prioritization_score)] = 0
senders_receivers = union(prioritized_tbl_oi$sender %>% unique(), prioritized_tbl_oi$receiver %>% unique()) %>% sort()
colors_sender = RColorBrewer::brewer.pal(n = length(senders_receivers), name = 'Spectral') %>% magrittr::set_names(senders_receivers)
colors_receiver = RColorBrewer::brewer.pal(n = length(senders_receivers), name = 'Spectral') %>% magrittr::set_names(senders_receivers)
circos_list = make_circos_group_comparison(prioritized_tbl_oi, colors_sender, colors_receiver)
Whereas these ChordDiagrams show the most specific interactions per group, they don't give insights into the data behind these predictions. Therefore we will now look at visualizations that indicate the different prioritization criteria used in MultiNicheNet.
In the next type of plots, we will 1) visualize the per-sample scaled product of normalized ligand and receptor pseudobulk expression, 2) visualize the scaled ligand activities, 3) cell-type specificity.
We will now check the top 50 interactions specific for the Tumor-tissue
group_oi = "idiopathic.pulmonary.fibrosis"prioritized_tbl_oi_IPF_50 = get_top_n_lr_pairs(
multinichenet_output$prioritization_tables,
top_n = 50,
groups_oi = group_oi)plot_oi = make_sample_lr_prod_activity_plots(
multinichenet_output$prioritization_tables,
prioritized_tbl_oi_IPF_50)
plot_oi
As a further help for further prioritization, we can assess the level of curation of these LR pairs as defined by the Intercellular Communication part of the Omnipath database
prioritized_tbl_oi_IPF_50_omnipath = prioritized_tbl_oi_IPF_50 %>%
inner_join(lr_network_all)Now we add this to the bubble plot visualization:
plot_oi = make_sample_lr_prod_activity_plots_Omnipath(
multinichenet_output$prioritization_tables,
prioritized_tbl_oi_IPF_50_omnipath)
plot_oi
Further note: Typically, there are way more than 50 differentially expressed and active ligand-receptor pairs per group across all sender-receiver combinations. Therefore it might be useful to zoom in on specific cell types as senders/receivers:
Eg CD16..Monocyte as receiver:
prioritized_tbl_oi_IPF_50 = get_top_n_lr_pairs(
multinichenet_output$prioritization_tables,
50,
groups_oi = group_oi,
receivers_oi = "CD16..Monocyte")plot_oi = make_sample_lr_prod_activity_plots_Omnipath(
multinichenet_output$prioritization_tables,
prioritized_tbl_oi_IPF_50 %>% inner_join(lr_network_all))
plot_oi
Eg CD14.Monocyte as sender:
prioritized_tbl_oi_IPF_50 = get_top_n_lr_pairs(
multinichenet_output$prioritization_tables,
50,
groups_oi = group_oi,
senders_oi = "CD16..Monocyte")plot_oi = make_sample_lr_prod_activity_plots_Omnipath(
multinichenet_output$prioritization_tables,
prioritized_tbl_oi_IPF_50 %>% inner_join(lr_network_all))
plot_oi
You can make these plots also for the other groups, like we will illustrate now for the S group
group_oi = "normal"prioritized_tbl_oi_Normal_50 = get_top_n_lr_pairs(
multinichenet_output$prioritization_tables,
50,
groups_oi = group_oi)
plot_oi = make_sample_lr_prod_activity_plots_Omnipath(
multinichenet_output$prioritization_tables,
prioritized_tbl_oi_Normal_50 %>% inner_join(lr_network_all))
plot_oi
Note: We can use make_sample_lr_prod_activity_batch_plots to visualize batches on this plot!
plot_oi = make_sample_lr_prod_activity_batch_plots(
multinichenet_output$prioritization_tables,
prioritized_tbl_oi_IPF_50,
multinichenet_output$grouping_tbl,
batches)
plot_oi
In another type of plot, we can visualize the ligand activities for a group-receiver combination, and show the predicted ligand-target links, and also the expression of the predicted target genes across samples.
For this, we now need to define a receiver cell type of interest. As example, we will take CLEC9A cells as receiver, and look at the top 10 senderLigand-receiverReceptor pairs with these cells as receiver.
group_oi = "idiopathic.pulmonary.fibrosis"
receiver_oi = "CD16..Monocyte"
prioritized_tbl_oi_IPF_10 = get_top_n_lr_pairs(
multinichenet_output$prioritization_tables,
10,
groups_oi = group_oi,
receivers_oi = receiver_oi)combined_plot = make_ligand_activity_target_plot(
group_oi,
receiver_oi,
prioritized_tbl_oi_IPF_10,
multinichenet_output$prioritization_tables,
multinichenet_output$ligand_activities_targets_DEgenes, contrast_tbl,
multinichenet_output$grouping_tbl,
multinichenet_output$celltype_info,
ligand_target_matrix,
plot_legend = FALSE)
combined_plot
## $combined_plot
##
## $legends
What if there is a specific ligand you are interested in?
group_oi = "idiopathic.pulmonary.fibrosis"
receiver_oi = "CD16..Monocyte"
ligands_oi = c("BMP1","BMP4","BMP5")
prioritized_tbl_ligands_oi = get_top_n_lr_pairs(
multinichenet_output$prioritization_tables,
10000,
groups_oi = group_oi,
receivers_oi = receiver_oi
) %>% filter(ligand %in% ligands_oi) # ligands should still be in the output tables of coursecombined_plot = make_ligand_activity_target_plot(
group_oi,
receiver_oi,
prioritized_tbl_ligands_oi,
multinichenet_output$prioritization_tables,
multinichenet_output$ligand_activities_targets_DEgenes,
contrast_tbl,
multinichenet_output$grouping_tbl,
multinichenet_output$celltype_info,
ligand_target_matrix,
plot_legend = FALSE)
combined_plot
## $combined_plot
##
## $legends
In the previous plots, target genes were shown that are predicted as target gene of ligands based on prior knowledge. However, we can use the multi-sample nature of this data to filter target genes based on expression correlation between the upstream ligand-receptor pair and the downstream target gene. We will filter out correlated ligand-receptor --> target links that both show high expression correlation (spearman or pearson correlation > 0.50 in this example) and have some prior knowledge to support their link. Note that you can only make these visualization if you ran step 7 of the core MultiNicheNet analysis.
group_oi = "idiopathic.pulmonary.fibrosis"
receiver_oi = "CD16..Monocyte"
lr_target_prior_cor_filtered = multinichenet_output$lr_target_prior_cor %>%
inner_join(
multinichenet_output$ligand_activities_targets_DEgenes$ligand_activities %>%
distinct(ligand, target, direction_regulation, contrast)
) %>%
inner_join(contrast_tbl) %>% filter(group == group_oi, receiver == receiver_oi)
lr_target_prior_cor_filtered_up = lr_target_prior_cor_filtered %>%
filter(direction_regulation == "up") %>%
filter( (rank_of_target < top_n_target) & (pearson > 0.50 | spearman > 0.50))
lr_target_prior_cor_filtered_down = lr_target_prior_cor_filtered %>%
filter(direction_regulation == "down") %>%
filter( (rank_of_target < top_n_target) & (pearson < -0.50 | spearman < -0.50)) # downregulation -- negative correlation
lr_target_prior_cor_filtered = bind_rows(
lr_target_prior_cor_filtered_up,
lr_target_prior_cor_filtered_down)Now we will visualize the top correlated target genes for the LR pairs that are also in the top 50 LR pairs discriminating the groups from each other:
prioritized_tbl_oi = get_top_n_lr_pairs(
multinichenet_output$prioritization_tables,
50,
groups_oi = group_oi,
receivers_oi = receiver_oi)lr_target_correlation_plot = make_lr_target_correlation_plot(
multinichenet_output$prioritization_tables,
prioritized_tbl_oi,
lr_target_prior_cor_filtered ,
multinichenet_output$grouping_tbl,
multinichenet_output$celltype_info,
receiver_oi,
plot_legend = FALSE)
lr_target_correlation_plot$combined_plot
You can also visualize the expression correlation in the following way for a selected LR pair and their targets:
ligand_oi = "CXCL12"
receptor_oi = "CXCR4"
sender_oi = "Fibroblast"
receiver_oi = "CD16..Monocyte"
lr_target_scatter_plot = make_lr_target_scatter_plot(
multinichenet_output$prioritization_tables,
ligand_oi, receptor_oi, sender_oi, receiver_oi,
multinichenet_output$celltype_info,
multinichenet_output$grouping_tbl,
lr_target_prior_cor_filtered)
lr_target_scatter_plot
In the plots before, we demonstrated that some DE genes have both expression correlation and prior knowledge support to be downstream of ligand-receptor pairs. Interestingly, some target genes can be ligands or receptors themselves. This illustrates that cells can send signals to other cells, who as a response to these signals produce signals themselves to feedback to the original sender cells, or who will effect other cell types.
As last plot, we can generate a 'systems' view of these intercellular feedback and cascade processes than can be occuring between the different cell populations involved. In this plot, we will draw links between ligands of sender cell types their ligand/receptor-annotated target genes in receiver cell types. So links are ligand-target links (= gene regulatory links) and not ligand-receptor protein-protein interactions! We will infer this intercellular regulatory network here for the top100 interactions. You can increase this to include more hits of course (recommended).
prioritized_tbl_oi = get_top_n_lr_pairs(
multinichenet_output$prioritization_tables,
100,
rank_per_group = FALSE)
lr_target_prior_cor_filtered =
multinichenet_output$prioritization_tables$group_prioritization_tbl$group %>% unique() %>%
lapply(function(group_oi){
lr_target_prior_cor_filtered = multinichenet_output$lr_target_prior_cor %>%
inner_join(
multinichenet_output$ligand_activities_targets_DEgenes$ligand_activities %>%
distinct(ligand, target, direction_regulation, contrast)
) %>%
inner_join(contrast_tbl) %>% filter(group == group_oi)
lr_target_prior_cor_filtered_up = lr_target_prior_cor_filtered %>%
filter(direction_regulation == "up") %>%
filter( (rank_of_target < top_n_target) & (pearson > 0.50 | spearman > 0.50))
lr_target_prior_cor_filtered_down = lr_target_prior_cor_filtered %>%
filter(direction_regulation == "down") %>%
filter( (rank_of_target < top_n_target) & (pearson < -0.50 | spearman < -0.50))
lr_target_prior_cor_filtered = bind_rows(
lr_target_prior_cor_filtered_up,
lr_target_prior_cor_filtered_down
)
}) %>% bind_rows()
lr_target_df = lr_target_prior_cor_filtered %>%
distinct(group, sender, receiver, ligand, receptor, id, target, direction_regulation) network = infer_intercellular_regulatory_network(lr_target_df, prioritized_tbl_oi)
network$links %>% head()
## # A tibble: 6 × 6
## sender_ligand receiver_target direction_regulation group type weight
## <chr> <chr> <fct> <chr> <chr> <dbl>
## 1 Fibroblast_A2M Fibroblast_A2M up idiopathic.pulmonary.fibrosis Ligand-Target 1
## 2 Fibroblast_A2M Fibroblast_FN1 up idiopathic.pulmonary.fibrosis Ligand-Target 1
## 3 Proliferating.Macrophage_SPP1 Fibroblast_FN1 up idiopathic.pulmonary.fibrosis Ligand-Target 1
## 4 Proliferating.Macrophage_FN1 Fibroblast_FN1 up idiopathic.pulmonary.fibrosis Ligand-Target 1
## 5 Fibroblast_FN1 Fibroblast_FN1 up idiopathic.pulmonary.fibrosis Ligand-Target 1
## 6 Fibroblast_COL1A1 Fibroblast_A2M up idiopathic.pulmonary.fibrosis Ligand-Target 1
network$nodes %>% head()
## # A tibble: 6 × 4
## node celltype gene type_gene
## <chr> <chr> <chr> <chr>
## 1 Fibroblast_MMP2 Fibroblast MMP2 ligand/receptor
## 2 Proliferating.Macrophage_MMP9 Proliferating.Macrophage MMP9 ligand/receptor
## 3 CD16..Monocyte_SELL CD16..Monocyte SELL ligand/receptor
## 4 CD16..Monocyte_SELPLG CD16..Monocyte SELPLG ligand/receptor
## 5 Proliferating.Macrophage_CD44 Proliferating.Macrophage CD44 ligand/receptor
## 6 Fibroblast_A2M Fibroblast A2M ligandnetwork_graph = visualize_network(network, colors_sender)
network_graph$plot
Interestingly, we can also use this network to further prioritize differential CCC interactions. Here we will assume that the most important LR interactions are the ones that are involved in this intercellular regulatory network. We can get these interactions as follows:
network$prioritized_lr_interactions
## # A tibble: 60 × 5
## group sender receiver ligand receptor
## <chr> <chr> <chr> <chr> <chr>
## 1 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast A2M MMP2
## 2 idiopathic.pulmonary.fibrosis Proliferating.Macrophage Fibroblast SPP1 ITGA8
## 3 idiopathic.pulmonary.fibrosis Proliferating.Macrophage Fibroblast FN1 ITGA8
## 4 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast FN1 ITGA8
## 5 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast FN1 SDC2
## 6 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast COL1A1 ITGA1
## 7 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast SLIT3 ROBO2
## 8 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast COL6A3 ITGA1
## 9 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast COL4A1 ITGB1
## 10 idiopathic.pulmonary.fibrosis CD16..Monocyte Fibroblast ITM2B ROR2
## # ℹ 50 more rowsprioritized_tbl_oi_network = prioritized_tbl_oi %>% inner_join(
network$prioritized_lr_interactions)
prioritized_tbl_oi_network
## # A tibble: 60 × 8
## group sender receiver ligand receptor id prioritization_score prioritization_rank
## <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
## 1 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast ITM2B ROR2 ITM2B_ROR2_Fibroblast_Fibroblast 0.912 1
## 2 normal CD16..Monocyte CD16..Monocyte IL10 IL10RA IL10_IL10RA_CD16..Monocyte_CD16..Monocyte 0.910 2
## 3 idiopathic.pulmonary.fibrosis Fibroblast Proliferating.Macrophage COL14A1 CD44 COL14A1_CD44_Fibroblast_Proliferating.Macrophage 0.907 5
## 4 idiopathic.pulmonary.fibrosis Fibroblast CD16..Monocyte CXCL12 CXCR4 CXCL12_CXCR4_Fibroblast_CD16..Monocyte 0.906 6
## 5 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast BMP4 ACVR1 BMP4_ACVR1_Fibroblast_Fibroblast 0.904 7
## 6 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast A2M MMP2 A2M_MMP2_Fibroblast_Fibroblast 0.903 8
## 7 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast SLIT3 ROBO2 SLIT3_ROBO2_Fibroblast_Fibroblast 0.898 10
## 8 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast SLIT3 ROBO1 SLIT3_ROBO1_Fibroblast_Fibroblast 0.898 11
## 9 idiopathic.pulmonary.fibrosis Proliferating.Macrophage Proliferating.Macrophage SPP1 CD44 SPP1_CD44_Proliferating.Macrophage_Proliferating.Macrophage 0.895 12
## 10 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast COL6A3 ITGA1 COL6A3_ITGA1_Fibroblast_Fibroblast 0.895 13
## # ℹ 50 more rowsVisualize now the expression and activity of these interactions for the Tumor group
group_oi = "idiopathic.pulmonary.fibrosis"prioritized_tbl_oi_IPF = prioritized_tbl_oi_network %>% filter(group == group_oi)
plot_oi = make_sample_lr_prod_activity_plots_Omnipath(
multinichenet_output$prioritization_tables,
prioritized_tbl_oi_IPF %>% inner_join(lr_network_all)
)
plot_oi
To assess how much difference the batch correction made, we will now run the MultiNicheNet analysis without batch correction with the wrapper function using the same parameters, and saving these analysis results in multinichenet_output_noBC
batches = NA
multinichenet_output_noBC = multi_nichenet_analysis(
sce = sce,
celltype_id = celltype_id, sample_id = sample_id, group_id = group_id,
batches = batches, covariates = covariates,
lr_network = lr_network, ligand_target_matrix = ligand_target_matrix,
contrasts_oi = contrasts_oi, contrast_tbl = contrast_tbl,
senders_oi = senders_oi, receivers_oi = receivers_oi,
min_cells = min_cells,
fraction_cutoff = fraction_cutoff,
min_sample_prop = min_sample_prop,
scenario = "regular",
ligand_activity_down = ligand_activity_down,
logFC_threshold = logFC_threshold,
p_val_threshold = p_val_threshold,
p_val_adj = p_val_adj,
empirical_pval = empirical_pval,
top_n_target = top_n_target,
n.cores = n.cores,
verbose = TRUE
)
## [1] "Cell type & sample filtering"
## [1] "condition-specific celltypes:"
## character(0)
## [1] "absent celltypes:"
## character(0)
## [1] "Gene filtering"
## [1] "Samples are considered if they have more than 10 cells of the cell type of interest"
## [1] "Genes with non-zero counts in at least 5% of cells of a cell type of interest in a particular sample will be considered as expressed in that sample."
## [1] "Genes expressed in at least 6 samples will considered as expressed in the cell type: Alveolar.Epithelial.Type.1"
## [1] "Genes expressed in at least 16 samples will considered as expressed in the cell type: CD16..Monocyte"
## [1] "Genes expressed in at least 16 samples will considered as expressed in the cell type: Fibroblast"
## [1] "Genes expressed in at least 6.5 samples will considered as expressed in the cell type: Proliferating.Macrophage"
## [1] "10193 genes are considered as expressed in the cell type: Alveolar.Epithelial.Type.1"
## [1] "8810 genes are considered as expressed in the cell type: CD16..Monocyte"
## [1] "10643 genes are considered as expressed in the cell type: Fibroblast"
## [1] "11018 genes are considered as expressed in the cell type: Proliferating.Macrophage"
## [1] "Calculate normalized average and pseudobulk expression"
## [1] "Calculate differential expression for all cell types"
## [1] "DE analysis is done:"
## [1] "included cell types are:"
## [1] "CD16..Monocyte" "Alveolar.Epithelial.Type.1" "Fibroblast" "Proliferating.Macrophage"
## [1] "retained cell types"
## [1] "CD16..Monocyte" "Alveolar.Epithelial.Type.1" "Fibroblast" "Proliferating.Macrophage"
## [1] "Calculate NicheNet ligand activities and ligand-target links"
## [1] "Combine all the information in prioritization tables"
## [1] "Calculate correlation between LR pairs and target genes"
## [1] "There are no condition specific cell types in the data. MultiNicheNet analysis is performed in the regular way for all cell types."First we will show the top 50 interactions from the batch-corrected analysis (BC analysis) with non-corrected pseudobulk expression values
group_oi = "idiopathic.pulmonary.fibrosis"
batches = "dataset_origin"prioritized_tbl_oi_top_50 = get_top_n_lr_pairs(
multinichenet_output$prioritization_tables,
50,
groups_oi = group_oi) # from BC-analysis
plot_oi = make_sample_lr_prod_activity_batch_plots(
multinichenet_output_noBC$prioritization_tables,
prioritized_tbl_oi_top_50,
multinichenet_output$grouping_tbl,
batches)
plot_oi
For this dataset and these cell types, the non-corrected expression values look similar to the corrected ones.
Now we will combine the prioritization tables of both analyses. This will then later be used to define which interactions are most specific to the BC analysis compared to the non-BC analysis
prioritized_tbl_oi_high5000_withBC = get_top_n_lr_pairs(
multinichenet_output$prioritization_tables,
5000,
rank_per_group = FALSE
)
prioritized_tbl_oi_high5000_noBC = get_top_n_lr_pairs(
multinichenet_output_noBC$prioritization_tables,
5000,
rank_per_group = FALSE
)
prioritized_tbl_oi_high5000 = prioritized_tbl_oi_high5000_withBC %>%
rename(score_BC = prioritization_score , rank_BC = prioritization_rank) %>%
full_join(
prioritized_tbl_oi_high5000_noBC %>%
rename(score_noBC = prioritization_score , rank_noBC = prioritization_rank)
)
head(prioritized_tbl_oi_high5000) # you can see some interactions NA in an analysis: this because ligand or receptor gene was filtered out
## # A tibble: 6 × 10
## group sender receiver ligand receptor id score_BC rank_BC score_noBC rank_noBC
## <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
## 1 idiopathic.pulmonary.fibrosis Fibroblast Fibroblast ITM2B ROR2 ITM2B_ROR2_Fibroblast_Fibroblast 0.912 1 0.892 6
## 2 normal CD16..Monocyte CD16..Monocyte IL10 IL10RA IL10_IL10RA_CD16..Monocyte_CD16..Monocyte 0.910 2 0.910 2
## 3 idiopathic.pulmonary.fibrosis Fibroblast CD16..Monocyte TGM2 ITGA4 TGM2_ITGA4_Fibroblast_CD16..Monocyte 0.908 3 0.796 421
## 4 idiopathic.pulmonary.fibrosis Fibroblast CD16..Monocyte CXCL14 CXCR4 CXCL14_CXCR4_Fibroblast_CD16..Monocyte 0.908 4 0.889 9
## 5 idiopathic.pulmonary.fibrosis Fibroblast Proliferating.Macrophage COL14A1 CD44 COL14A1_CD44_Fibroblast_Proliferating.Macrophage 0.907 5 0.896 5
## 6 idiopathic.pulmonary.fibrosis Fibroblast CD16..Monocyte CXCL12 CXCR4 CXCL12_CXCR4_Fibroblast_CD16..Monocyte 0.906 6 0.926 1
prioritized_tbl_oi_high5000 = prioritized_tbl_oi_high5000 %>%
mutate(
diff_rank = rank_BC - rank_noBC,
diff_score = score_BC - score_noBC) Inspecting prioritized_tbl_oi_high5000 enables you to see how prioritization scores and ranks differ between both analyses.
prioritized_tbl_oi_high5000 %>% View()Now we will define which interactions are most specific to the BC analysis compared to the non-BC analysis
BC_interactions = prioritized_tbl_oi_high5000 %>%
arrange(-diff_score) %>%
filter(group == group_oi) %>%
filter(rank_BC < 2000) %>%
pull(id) %>%
head(10)
noBC_interactions = prioritized_tbl_oi_high5000 %>%
arrange(diff_score) %>%
filter(group == group_oi) %>%
filter(rank_noBC < 2000) %>%
pull(id) %>%
head(10)
BC_interactions_df = prioritized_tbl_oi_high5000 %>%
arrange(-score_BC) %>%
filter(is.na(diff_rank)) %>%
filter(group == group_oi) %>%
head(10)
noBC_interactions_df = prioritized_tbl_oi_high5000 %>%
arrange(-score_noBC) %>%
filter(is.na(diff_rank)) %>%
filter(group == group_oi) %>%
head(10)
BC_specific_interactions_df = prioritized_tbl_oi_high5000 %>%
arrange(-score_BC) %>%
filter(group == group_oi) %>%
filter(id %in% BC_interactions)
noBC_specific_interactions_df = prioritized_tbl_oi_high5000 %>%
arrange(-score_noBC) %>%
filter(group == group_oi) %>%
filter(id %in% noBC_interactions)plot_oi = make_sample_lr_prod_activity_batch_plots(
multinichenet_output$prioritization_tables,
BC_specific_interactions_df,
multinichenet_output$grouping_tbl,
batches)
plot_oi
plot_oi = make_sample_lr_prod_activity_batch_plots(
multinichenet_output_noBC$prioritization_tables,
BC_specific_interactions_df,
multinichenet_output$grouping_tbl,
batches)
plot_oi
You can here indeed see the clear effects of the source-dataset in expression levels of some interactions (which may cloud the true DE signal that we pick up after correction).
plot_oi = make_sample_lr_prod_activity_batch_plots(
multinichenet_output$prioritization_tables,
noBC_specific_interactions_df,
multinichenet_output$grouping_tbl,
batches)
plot_oi
plot_oi = make_sample_lr_prod_activity_batch_plots(
multinichenet_output_noBC$prioritization_tables,
noBC_specific_interactions_df,
multinichenet_output$grouping_tbl,
batches)
plot_oi
Important to note is that the interactions we visualize here were prioritized also by including ligand activity, so not only the DE of the LR pair! However, ligand activity may also be affected by batch effect correction because the underlying DE genes in receivers is affected by batch effect correction. Therefore, we will now check the effect of the dataset of origin on gene expression of some DE genes
Show now also DE genes that are different! - this is important for the ligand activities!
pval_df_targets = multinichenet_output_noBC$celltype_de %>%
filter(contrast == "idiopathic.pulmonary.fibrosis-normal") %>%
select(gene, cluster_id, p_adj, logFC) %>%
distinct() %>%
rename(p_adj_noBC = p_adj, logFC_noBC = logFC) %>%
inner_join(
multinichenet_output$celltype_de %>%
filter(contrast == "idiopathic.pulmonary.fibrosis-normal") %>%
select(gene, cluster_id, p_adj, logFC) %>%
distinct() %>%
rename(p_adj_BC = p_adj, logFC_BC = logFC)
)
## targets with more DE in noBC condition
pval_df_targets %>%
filter(logFC_noBC > 0) %>%
mutate(prop = p_adj_BC/p_adj_noBC, prop_logFC = logFC_noBC/logFC_BC) %>%
mutate(prop_pval_logFC = prop*prop_logFC) %>%
arrange(-prop_pval_logFC) %>%
filter(prop > 1 & p_adj_noBC < 0.05 & p_adj_BC > 0.05)
## # A tibble: 19 × 9
## gene cluster_id p_adj_noBC logFC_noBC p_adj_BC logFC_BC prop prop_logFC prop_pval_logFC
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 CCL21 Fibroblast 0.0102 2.39 0.462 0.783 45.3 3.05 138.
## 2 FST Fibroblast 0.013 1.76 0.324 0.691 24.9 2.55 63.5
## 3 TREM2 Alveolar.Epithelial.Type.1 0.00418 2.98 0.0794 1.88 19.0 1.59 30.1
## 4 COL5A2 Fibroblast 0.0469 0.613 0.224 0.383 4.78 1.60 7.64
## 5 SPP1 Alveolar.Epithelial.Type.1 0.0252 2.67 0.104 1.69 4.13 1.58 6.52
## 6 SERPINE1 Fibroblast 0.0427 1.23 0.143 0.9 3.35 1.37 4.58
## 7 DTNA Fibroblast 0.0231 1.05 0.0743 0.742 3.22 1.42 4.55
## 8 PDE4B Fibroblast 0.0193 0.859 0.056 0.601 2.90 1.43 4.15
## 9 PPARG Fibroblast 0.0311 1.02 0.0747 0.711 2.40 1.43 3.45
## 10 PDGFC Fibroblast 0.0433 0.772 0.0871 0.511 2.01 1.51 3.04
## 11 ACSL4 Fibroblast 0.0228 1.02 0.0534 0.834 2.34 1.22 2.86
## 12 ITGA11 Fibroblast 0.044 0.82 0.086 0.62 1.95 1.32 2.59
## 13 TNFRSF10D Fibroblast 0.0311 1.1 0.0617 0.908 1.98 1.21 2.40
## 14 C4orf48 Fibroblast 0.0378 0.679 0.0701 0.527 1.85 1.29 2.39
## 15 SDC2 Fibroblast 0.047 0.568 0.0903 0.477 1.92 1.19 2.29
## 16 NLGN4Y Fibroblast 0.0431 1.32 0.0623 1.09 1.45 1.21 1.75
## 17 MSRB3 Proliferating.Macrophage 0.0421 2.47 0.0543 2.31 1.29 1.07 1.38
## 18 AMPD3 Proliferating.Macrophage 0.0478 1.75 0.0518 1.39 1.08 1.26 1.36
## 19 RSPH3 Fibroblast 0.047 0.706 0.0521 0.644 1.11 1.10 1.22
pval_df_targets %>%
filter(logFC_noBC > 0) %>%
mutate(prop = p_adj_BC/p_adj_noBC, prop_logFC = logFC_noBC/logFC_BC) %>%
mutate(prop_pval_logFC = prop*prop_logFC) %>%
arrange(-prop_pval_logFC) %>%
filter(prop > 1 & p_adj_noBC < 0.05 & p_adj_BC > 0.05) %>%
group_by(cluster_id) %>%
count() %>%
arrange(-n)
## # A tibble: 3 × 2
## # Groups: cluster_id [3]
## cluster_id n
## <chr> <int>
## 1 Fibroblast 15
## 2 Alveolar.Epithelial.Type.1 2
## 3 Proliferating.Macrophage 2
## targets with more DE in BC condition
pval_df_targets %>%
filter(logFC_BC > 0) %>%
mutate(prop = p_adj_BC/p_adj_noBC, prop_logFC = logFC_noBC/logFC_BC) %>%
mutate(prop_pval_logFC = prop*prop_logFC) %>%
arrange(prop_pval_logFC) %>%
filter(prop < 1 & p_adj_noBC > 0.05 & p_adj_BC < 0.05)
## # A tibble: 178 × 9
## gene cluster_id p_adj_noBC logFC_noBC p_adj_BC logFC_BC prop prop_logFC prop_pval_logFC
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 MCL1 CD16..Monocyte 0.94 -0.274 0.0425 0.532 0.0452 -0.515 -0.0233
## 2 MYLK Fibroblast 0.741 -0.262 0.0455 0.817 0.0614 -0.321 -0.0197
## 3 TGM2 Fibroblast 0.679 -0.29 0.0217 0.694 0.0320 -0.418 -0.0134
## 4 MCL1 Fibroblast 0.861 -0.319 0.0147 0.811 0.0171 -0.393 -0.00672
## 5 CD81 Fibroblast 0.993 -0.00883 0.00615 0.54 0.00619 -0.0164 -0.000101
## 6 TSC22D1 Fibroblast 0.144 0.578 0.0000329 1 0.000228 0.578 0.000132
## 7 A2M Fibroblast 0.426 0.534 0.000148 1.32 0.000347 0.405 0.000141
## 8 ITM2B CD16..Monocyte 0.554 0.292 0.000945 0.58 0.00171 0.503 0.000859
## 9 FHL1 Fibroblast 0.968 0.0367 0.0165 0.613 0.0170 0.0599 0.00102
## 10 WLS Fibroblast 0.0636 0.651 0.000112 0.841 0.00176 0.774 0.00136
## # ℹ 168 more rows
pval_df_targets %>%
filter(logFC_BC > 0) %>%
mutate(prop = p_adj_BC/p_adj_noBC, prop_logFC = logFC_noBC/logFC_BC) %>%
mutate(prop_pval_logFC = prop*prop_logFC) %>%
arrange(prop_pval_logFC) %>%
filter(prop < 1 & p_adj_noBC > 0.05 & p_adj_BC < 0.05) %>%
group_by(cluster_id) %>%
count() %>%
arrange(-n)
## # A tibble: 4 × 2
## # Groups: cluster_id [4]
## cluster_id n
## <chr> <int>
## 1 Fibroblast 59
## 2 CD16..Monocyte 43
## 3 Proliferating.Macrophage 41
## 4 Alveolar.Epithelial.Type.1 35Define BC-specific DE genes in Fibroblast
targets_oi = pval_df_targets %>%
filter(logFC_BC > 0) %>%
mutate(prop = p_adj_BC/p_adj_noBC, prop_logFC = logFC_noBC/logFC_BC) %>%
mutate(prop_pval_logFC = prop*prop_logFC) %>%
arrange(prop_pval_logFC) %>%
filter(p_adj_noBC > 0.05 & p_adj_BC < 0.05) %>%
filter(cluster_id == "Fibroblast") %>%
pull(gene) %>% head(5)
targets_oi %>% tibble(gene = .)
## # A tibble: 5 × 1
## gene
## <chr>
## 1 MYLK
## 2 TGM2
## 3 MCL1
## 4 CD81
## 5 TSC22D1Visualize these BC_specific_targets with corrected expression values:
p_target = make_DEgene_dotplot_pseudobulk_batch(
genes_oi = targets_oi,
celltype_info = multinichenet_output$celltype_info,
prioritization_tables = multinichenet_output$prioritization_tables,
celltype_oi = "Fibroblast",
batch_oi = batches,
grouping_tbl = multinichenet_output$grouping_tbl)
p_target$pseudobulk_plot
Visualize these BC_specific_targets with non-corrected expression values:
p_target = make_DEgene_dotplot_pseudobulk_batch(
genes_oi = targets_oi,
celltype_info = multinichenet_output_noBC$celltype_info,
prioritization_tables = multinichenet_output_noBC$prioritization_tables,
celltype_oi = "Fibroblast",
batch_oi = batches,
grouping_tbl = multinichenet_output$grouping_tbl)
p_target$pseudobulk_plot
Based on these plots, we can appreciate why they were DE more strongly after correction that before.
All together, these comparisons demonstrate that it is advisable to perform batch correction when possible.