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Breast_Cancer
Breast_Cancer
 
 
IPF
IPF
 
 
MOB
MOB
 
 
Melanoma
Melanoma
 
 
Simulation
Simulation
 
 
Simulation_seq_based
Simulation_seq_based
 
 
README.md
README.md
 
 

README.md

Figures

This folder contains R Notebooks used for creating figures in the manuscript.

Simulation Studies

STARmap-based simulation

generate_simulation_figures.nb.html:

  • Figure 2A. Visualization of STARmap dataset
  • Figure 2B. Performance of all methods in Scenario 1
  • Figure 2C. Heatmap of proportion of eL2/3 in the simulated spatial pseudo-spots
  • Figure 2D. Performance of all methods with External reference in Scenario 1~3
  • Figure S1. Heatmap of proportions of 4 cell types in the simulated spatial pseudo-spots
  • Figure S2. Correlations between proportions of all cell types in Scenario 1

Sequencing-based simulation

generate_seq_based_simulation_figures.nb.html:

  • Figure S5. Boxplot of performance of all methods in sequencing-based simulation

Simulation for rare cell types

generate_simulation_Oligo_figures.nb.html:

  • Figure S3. Performance of Oligo cell type deconvolution in STARmap-based simulation

  • Figure S4. Performance of Oligo cell type deconvolution in settings with down sampled Oligo cells in reference for the STARmap-based simulation

Simulation for high cell density

generate_seq_based_high_density_figures.nb.html:

  • Figure S6. Performance of SDePER and GLRM in simulation for high cell density

Ablation tests

generate_ablation_figures.nb.html:

  • Figure S7. Performance in Ablation test in STARmap-based simulation
  • Figure S8. Performance in Ablation test in sequencing-based simulation study
  • Figure S9. Performance in Ablation test in STARmap-based simulation with a subset of 5 cell types

Real Dataset Analysis

Mouse Olfactory Bulb (MOB)

generate_MOB_figures.nb.html:

  • Figure 3A. Visualization of MOB dataset
  • Figure 3B. Visualization of inferred dominant cell type in each spot
  • Figure 3C. Visualization of inferred cell type proportions in each spot
  • Figure 3D. ARI and purity of all methods
  • Figure 3E. Heatmap of original and imputed expression of 4 layer-specific marker genes
  • Figure 3F. Heatmap of average imputed expression of 4 layer-specific marker genes at 80 μm level
  • Figure 3G. Ratio of average imputed expression of 4 layer-specific marker genes at 80 μm level
  • Figure S11. Heatmap of 5 cell type-specific marker genes
  • Figure S12. Heatmap of estimated and imputed cell type proportions by SDePER and CARD
  • Figure S13. Heatmap of imputed expression of 4 layer-specific marker genes by SDePER and CARD

Melanoma

generate_Melanoma_figures.nb.html:

  • Figure 4A. Visualization of Melanoma dataset
  • Figure 4B. Visualization of inferred dominant cell type in each spot
  • Figure 4C. Visualization of inferred cell type proportions in each spot
  • Figure 4D. ARI and purity of all methods
  • Figure 4E. Heatmap of original and imputed expression of 4 region-specific marker genes
  • Figure 4F. Heatmap of average imputed expression of 4 region-specific marker genes at 80 μm level
  • Figure 4G. Ratio of average imputed expression of 4 region-specific marker genes at 80 μm level
  • Figure S14. Heatmap of 7 cell type-specific marker genes
  • Figure S16. Heatmap of estimated and imputed cell type proportions by SDePER and CARD
  • Figure S17. Heatmap of imputed expression of 4 region-specific marker genes by SDePER and CARD

Breast Cancer

generate_Breast_Cancer_figures.nb.html:

  • Figure 5A. Visualization of Breast Cancer dataset
  • Figure 5B. Visualization of inferred dominant cell type in each spot
  • Figure 5C. Visualization of inferred cell type proportions in each spot
  • Figure 5D. ARI and purity of all methods
  • Figure 5E. Heatmap of original and imputed expression of 4 region-specific marker genes
  • Figure 5F. Heatmap of average imputed expression of 4 region-specific marker genes at 80 μm level
  • Figure 5G. Ratio of average imputed expression of 4 region-specific marker genes at 80 μm level
  • Figure S18. Heatmap of 9 cell type-specific marker genes
  • Figure S20. Heatmap of estimated and imputed cell type proportions by SDePER and CARD
  • Figure S21. Heatmap of imputed expression of 4 region-specific marker genes by SDePER and CARD

Idiopathic Pulmonary Fibrosis (IPF) Lung

generate_IPF_figures.nb.html:

  • Figure 6B. Heatmap of 4 cell type-specific marker genes
  • Figure 6C. Visualization of inferred cell type proportions in each spot of 4 methods
  • Figure 6D. Weighted mean of expressions of 4 cell type-specific marker genes
  • Figure 6E. Heatmap of pairwise correlation of estimated cell type proportions
  • Figure S23. Visualization of inferred cell type proportions in each spot of all methods