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perf: improve spia script and report (#83)
These changes come from implementing spia in a GFOLD-based workflow here: https://github.com/dlaehnemann/rna-seq-conservative-fold-change-without-replicates This was modeled on the spia implementation here, and led to some cleanup of the `spia.R` script, to the removal of unnecessary report tables that didn't add any value and to some improvements of the spia reporting table.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,17 @@ | ||
| **Pathway enrichment** performed with SPIA, using the model ``{{ snakemake.config["diffexp"]["models"][snakemake.wildcards.model]["full"] }}``. | ||
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| 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. | ||
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| 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. |
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| @@ -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 |
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