perf: improve spia script and report

workflow/report/spia.rst

@@ -1,5 +1,17 @@
 **Pathway enrichment** performed with SPIA, using the model ``{{ snakemake.config["diffexp"]["models"][snakemake.wildcards.model]["full"] }}``.
 
-The table contains the following columns (also see the `SPIA docs <https://rdrr.io/bioc/SPIA/man/spia.html>`_): 
-``pSize`` is the number of genes on the pathway; ``NDE`` is the number of DE genes per pathway; ``tA`` is the observed total perturbation accumulation in the pathway; ``pNDE`` is the probability to observe at least NDE genes on the pathway using a hypergeometric model; ``pPERT`` is the probability to observe a total accumulation more extreme than tA only by chance; ``pG`` is the p-value obtained by combining pNDE and pPERT; ``pGFdr`` and ``pGFWER`` are the False Discovery Rate and respectively Bonferroni adjusted global p-values; and the ``Status`` gives the direction in which the pathway is perturbed (``activated`` or ``inhibited``). KEGGLINK gives a web link to the KEGG website that displays the pathway image with the differentially expressed genes highlighted in red.
+The table contains the following columns that have been renamed for descriptive titles (also see the `SPIA docs <https://rdrr.io/bioc/SPIA/man/spia.html>`_; for renamed columns, original spia column names are mentioned in parentheses): 
+**Name** of the pathway;
+**number of genes on the pathway** (``pSize``);
+**number of DE genes per pathway** where DE signifies "differentially expressed" (``NDE``);
+**total perturbation accumulation** (``tA``);
+**Combined FDR** where FDR signifies "false discovery rate" (``pGFdr``);
+**Status** of the pathway, inhibited vs. activated.
 
+The following columns (available from spia output), are hidden in this table in favour of the combined FDR as an overall assessment of the reliability of a pathway's perturbation.
+You can access them per pathway by clicking on the leading ``+`` symbol of a row:
+**p-value for at least NDE genes** where NDE signifies "n differentially expressed" (``pNDE``);
+**p-value to observe a total accumulation** (``pPERT``);
+**Combined p-value** (``pG``);
+**Combined Bonferroni p-values** (``pGFWER``);
+**pathway id** provided by the pathway database used.

workflow/resources/datavzrd/spia-template.yaml

@@ -1,181 +1,68 @@
-name: ?f"Pathway impact analysis for model {wildcards.model}"
+name: ?f"spia pathway impact analysis for model {wildcards.model}"
 datasets:
   spia_table:
     path: ?input.spia_table
     offer-excel: true
     separator: "\t"
-  spia_table_activated:
-    path: ?input.spia_table_activated
-    offer-excel: true
-    separator: "\t"
-  spia_table_inhibited:
-    path: ?input.spia_table_inhibited
-    offer-excel: true
-    separator: "\t"
 default-view: spia_table
 views:
   spia_table:
     dataset: spia_table
     desc: |
-        The table contains the following columns pSize is the number of genes on the pathway; NDE is the number of DE genes per pathway; tA is the observed total perturbation accumulation in the pathway; pNDE is the probability to observe at least NDE genes on the pathway using a hypergeometric model; pPERT is the probability to observe a total accumulation more extreme than tA only by chance; pG is the p-value obtained by combining pNDE and pPERT; pGFdr and pGFWER are the False Discovery Rate and respectively Bonferroni adjusted global p-values; and the Status gives the direction in which the pathway is perturbed (activated or inhibited).
+      ?f"spia pathway impact analysis for model {wildcards.model}"
     page-size: 25
     render-table:
       columns:
         Name:
           display-mode: normal
           link-to-url: 
-            reactome:
-              url: "http://reactome.org/PathwayBrowser/#/{Ids}"
+            pathway:
+              ?if params.pathway_db == "reactome":
+                url: "http://reactome.org/PathwayBrowser/#/{pathway id}"
+              ?elif params.pathway_db == "panther":
+                url: "https://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession={pathway id}"
+              # we should add all the pathway databases that bioconductor-graphite enables (see its `pathwayDatabases()` function)
+              ?else: # not sure what a good fallback would be here
+                url: "http://reactome.org/PathwayBrowser/#/{pathway id}"
         number of genes on the pathway:
           plot:
             heatmap:
               scale: linear
               range:
-                - white
-                - "#186904"        
+                - "#F7F7F7"
+                - "#B2182B"
         number of DE genes per pathway:
           plot:
             heatmap:
               scale: linear
               range:
-                - white
-                - "#186904"
+                - "#F7F7F7"
+                - "#B2182B"
         p-value for at least NDE genes:
-          display-mode: hidden
+          display-mode: detail
         total perturbation accumulation:
           plot:
             heatmap:
               scale: linear
               range:
-                - "#e6550d"
-                - "white"
-                - "#6baed6"
-              domain:
-                - -1
-                - 0
-                - 1
+                - "#B2182B"
+                - "#F7F7F7"
+                - "#2166AC"
+              domain-mid: 0
         p-value to observe a total accumulation:
-          display-mode: hidden
+          display-mode: detail
         Combined p-value:
-          display-mode: hidden
+          display-mode: detail
         Combined FDR:
           plot:
             bars:
               scale: linear
         Combined Bonferroni p-values:
-          display-mode: hidden     
+          display-mode: detail     
         Status:
           plot:
             heatmap:
               scale: ordinal
               color-scheme: accent
-        Ids:
-          display-mode: hidden
-  spia_table_activated:
-    dataset: spia_table_activated
-    desc: |
-        The table (sorted by "Status:Activated") contains the following columns pSize is the number of genes on the pathway; NDE is the number of DE genes per pathway; tA is the observed total perturbation accumulation in the pathway; pNDE is the probability to observe at least NDE genes on the pathway using a hypergeometric model; pPERT is the probability to observe a total accumulation more extreme than tA only by chance; pG is the p-value obtained by combining pNDE and pPERT; pGFdr and pGFWER are the False Discovery Rate and respectively Bonferroni adjusted global p-values; and the Status gives the direction in which the pathway is perturbed (activated).
-    page-size: 25
-    render-table:
-      columns:
-        Name:
-          display-mode: normal
-          link-to-url: 
-            reactome:
-              url: "http://reactome.org/PathwayBrowser/#/{Ids}"
-        number of genes on the pathway:
-          plot:
-            heatmap:
-              scale: linear
-              range:
-                - white
-                - "#186904"        
-        number of DE genes per pathway:
-          plot:
-            heatmap:
-              scale: linear
-              range:
-                - white
-                - "#186904"
-        p-value for at least NDE genes:
-          display-mode: hidden
-        total perturbation accumulation:
-          plot:
-            heatmap:
-              scale: linear
-              range:
-                - "#e6550d"
-                - "white"
-                - "#6baed6"
-              domain:
-                - -1
-                - 0
-                - 1
-        p-value to observe a total accumulation:
-          display-mode: hidden
-        Combined p-value:
-          display-mode: hidden
-        Combined FDR:
-          plot:
-            bars:
-              scale: linear
-        Combined Bonferroni p-values:
-          display-mode: hidden     
-        Status:
-          display-mode: normal
-        Ids:
-          display-mode: hidden 
-  spia_table_inhibited:
-    dataset: spia_table_inhibited
-    desc: |
-        The table (sorted by "Status:Inhibited") contains the following columns pSize is the number of genes on the pathway; NDE is the number of DE genes per pathway; tA is the observed total perturbation accumulation in the pathway; pNDE is the probability to observe at least NDE genes on the pathway using a hypergeometric model; pPERT is the probability to observe a total accumulation more extreme than tA only by chance; pG is the p-value obtained by combining pNDE and pPERT; pGFdr and pGFWER are the False Discovery Rate and respectively Bonferroni adjusted global p-values; and the Status gives the direction in which the pathway is perturbed (inhibited).
-    page-size: 25
-    render-table:
-      columns:
-        Name:
-          display-mode: normal
-          link-to-url: 
-            reactome:
-              url: "http://reactome.org/PathwayBrowser/#/{Ids}"
-        number of genes on the pathway:
-          plot:
-            heatmap:
-              scale: linear
-              range:
-                - white
-                - "#186904"        
-        number of DE genes per pathway:
-          plot:
-            heatmap:
-              scale: linear
-              range:
-                - white
-                - "#186904"
-        p-value for at least NDE genes:
-          display-mode: hidden
-        total perturbation accumulation:
-          plot:
-            heatmap:
-              scale: linear
-              range:
-                - "#e6550d"
-                - "white"
-                - "#6baed6"
-              domain:
-                - -1
-                - 0
-                - 1
-        p-value to observe a total accumulation:
-          display-mode: hidden
-        Combined p-value:
-          display-mode: hidden
-        Combined FDR:
-          plot:
-            bars:
-              scale: linear
-        Combined Bonferroni p-values:
-          display-mode: hidden     
-        Status:
-          display-mode: normal
-        Ids:
-          display-mode: hidden  
+        pathway id:
+          display-mode: detail

workflow/rules/datavzrd.smk

@@ -2,12 +2,12 @@ rule render_datavzrd_config_spia:
     input:
         template=workflow.source_path("../resources/datavzrd/spia-template.yaml"),
         spia_table="results/tables/pathways/{model}.pathways.tsv",
-        spia_table_activated="results/tables/pathways/{model}.activated-pathways.tsv",
-        spia_table_inhibited="results/tables/pathways/{model}.inhibited-pathways.tsv",
     output:
         "results/datavzrd/spia/{model}.yaml",
     log:
         "logs/yte/render-datavzrd-config-spia/{model}.log",
+    params:
+        pathway_db=config["enrichment"]["spia"]["pathway_database"],
     template_engine:
         "yte"
 
@@ -53,8 +53,6 @@ rule spia_datavzrd:
         config="results/datavzrd/spia/{model}.yaml",
         # files required for rendering the given configs
         spia_table="results/tables/pathways/{model}.pathways.tsv",
-        spia_table_activated="results/tables/pathways/{model}.activated-pathways.tsv",
-        spia_table_inhibited="results/tables/pathways/{model}.inhibited-pathways.tsv",
     output:
         report(
             directory("results/datavzrd-reports/spia-{model}"),
@@ -67,8 +65,7 @@ rule spia_datavzrd:
     log:
         "logs/datavzrd-report/spia-{model}/spia-{model}.log",
     wrapper:
-        # "v2.6.0/utils/datavzrd"
-        "v3.3.5-1-gd73914d/utils/datavzrd"
+        "v3.3.6/utils/datavzrd"
 
 
 rule diffexp_datavzrd:
@@ -93,8 +90,7 @@ rule diffexp_datavzrd:
     log:
         "logs/datavzrd-report/diffexp.{model}/diffexp.{model}.log",
     wrapper:
-        # "v2.6.0/utils/datavzrd"
-        "v3.3.5-1-gd73914d/utils/datavzrd"
+        "v3.3.6/utils/datavzrd"
 
 
 rule go_enrichment_datavzrd:
@@ -121,5 +117,4 @@ rule go_enrichment_datavzrd:
     log:
         "logs/datavzrd-report/go_enrichment-{model}/go_enrichment-{model}_{gene_fdr}.go_term_fdr_{go_term_fdr}.log",
     wrapper:
-        # "v2.6.0/utils/datavzrd"
-        "v3.3.5-1-gd73914d/utils/datavzrd"
+        "v3.3.6/utils/datavzrd"

workflow/rules/enrichment.smk

@@ -12,8 +12,6 @@ rule spia:
         spia_db="resources/spia-db.rds",
     output:
         table="results/tables/pathways/{model}.pathways.tsv",
-        table_activated="results/tables/pathways/{model}.activated-pathways.tsv",
-        table_inhibited="results/tables/pathways/{model}.inhibited-pathways.tsv",
         plots="results/plots/pathways/{model}.spia-perturbation-plots.pdf",
     params:
         bioc_species_pkg=bioc_species_pkg,