From 3843e0d1c0ae59fec927748adac122ae35e2f540 Mon Sep 17 00:00:00 2001 From: dlaehnemann Date: Thu, 16 Nov 2023 14:24:44 +0100 Subject: [PATCH 1/8] bring spia.R changes from gfold workflow here --- workflow/scripts/spia.R | 142 +++++++++++++++++++++------------------- 1 file changed, 76 insertions(+), 66 deletions(-) diff --git a/workflow/scripts/spia.R b/workflow/scripts/spia.R index dbd41a5f..a5b33289 100644 --- a/workflow/scripts/spia.R +++ b/workflow/scripts/spia.R @@ -6,9 +6,8 @@ library("SPIA") library("graphite") library(snakemake@params[["bioc_species_pkg"]], character.only = TRUE) -# provides library("tidyverse") and functions load_bioconductor_package() and -# get_prefix_col(), the latter requires snakemake@output[["samples"]] and -# snakemake@params[["covariate"]] +# provides library("tidyverse") and get_prefix_col(), where the latter requires +# snakemake@input[["samples"]] and snakemake@params[["covariate"]] source(snakemake@params[["common_src"]]) pw_db <- snakemake@params[["pathway_db"]] @@ -16,33 +15,45 @@ db <- readRDS(snakemake@input[["spia_db"]]) options(Ncpus = snakemake@threads) -diffexp <- read_tsv(snakemake@input[["diffexp"]]) %>% - drop_na(ens_gene) %>% - mutate(ens_gene = str_c("ENSEMBL:", ens_gene)) -universe <- diffexp %>% pull(var = ens_gene) -sig_genes <- diffexp %>% filter(qval <= 0.05) +diffexp <- read_tsv(snakemake@input[["diffexp"]]) |> + drop_na(ens_gene) |> + mutate(ens_gene = str_c("ENSEMBL:", ens_gene)) + +universe <- diffexp |> + dplyr::select(ens_gene) |> + distinct() |> + pull(ens_gene) + +sig_genes <- diffexp |> + filter(qval <= 0.05) + +columns <- c( + "Name", + "number of genes on the pathway", + "number of DE genes per pathway", + "p-value for at least NDE genes", + "total perturbation accumulation", + "p-value to observe a total accumulation", + "Combined p-value", + "Combined FDR", + "Combined Bonferroni p-values", + "Status", + "pathway id" +) + if (nrow(sig_genes) == 0) { - cols <- c( - "Name", "Status", "Combined FDR", - "total perturbation accumulation", "number of genes on the pathway", - "number of DE genes per pathway", "p-value for at least NDE genes", - "Combined Bonferroni p-values", - "p-value to observe a total accumulation", "Combined p-value", "Ids" - ) - res <- data.frame(matrix(ncol = 11, nrow = 0, dimnames = list(NULL, cols))) - # create empty perturbation plots - pdf(file = snakemake@output[["plots"]]) - write_tsv(res, snakemake@output[["table"]]) - write_tsv(res, snakemake@output[["table_activated"]]) - write_tsv(res, snakemake@output[["table_inhibited"]]) - dev.off() + # the best hack for an empty tibble from a column specification I could find + res <- read_csv("\n", col_names = columns) + write_tsv(res, snakemake@output[["table"]]) + write_tsv(res, snakemake@output[["table_activated"]]) + write_tsv(res, snakemake@output[["table_inhibited"]]) } else { # get logFC equivalent (the sum of beta scores of covariates of interest) beta_col <- get_prefix_col("b", colnames(sig_genes)) - beta <- sig_genes %>% - dplyr::select(ens_gene, !!beta_col) %>% + beta <- sig_genes |> + dplyr::select(ens_gene, !!beta_col) |> deframe() t <- tempdir(check = TRUE) @@ -50,8 +61,11 @@ if (nrow(sig_genes) == 0) { setwd(t) prepareSPIA(db, pw_db) res <- runSPIA( - de = beta, all = universe, pw_db, - plots = TRUE, verbose = TRUE + de = beta, + all = universe, + pw_db, + plots = TRUE, + verbose = TRUE ) setwd(olddir) @@ -60,47 +74,43 @@ if (nrow(sig_genes) == 0) { snakemake@output[["plots"]] ) pathway_names <- db[res$Name] - pathway_names <- db[res$Name] - path_ids <- as.matrix(lapply(pathway_names@entries, slot, "id")) - if (length(path_ids) > 0) { - path_ids_data_frame <- - data.frame(Ids = matrix(unlist(path_ids), - nrow = length(path_ids), byrow = TRUE - )) - final_res <- cbind(res, - Ids = path_ids_data_frame$Ids - ) - res_reorder <- dplyr::select( - final_res, Name, Status, - pGFdr, tA, pSize, NDE, pNDE, pGFWER, pPERT, pG, Ids - ) - res_reorder <- res_reorder %>% - rename( - "Combined Bonferroni p-values" = "pGFWER", - "Combined FDR" = "pGFdr", - "total perturbation accumulation" = "tA", - "number of genes on the pathway" = "pSize", - "number of DE genes per pathway" = "NDE", - "Combined p-value" = "pG", - "p-value to observe a total accumulation" = "pPERT", - "p-value for at least NDE genes" = "pNDE" + if (length(pathway_names) > 0) { + pathway_ids_tibble <- pathway_names@entries |> + map(slot, "id") |> + unlist() |> + as_tibble( + rownames="pathway_name" + ) |> + rename( + `pathway id` = value + ) + final_res <- as_tibble(res) |> + left_join( + pathway_ids_tibble, + join_by(Name == pathway_name) + ) |> + rename( + "number of genes on the pathway" = "pSize", + "number of DE genes per pathway" = "NDE", + "p-value for at least NDE genes" = "pNDE", + "total perturbation accumulation" = "tA", + "p-value to observe a total accumulation" = "pPERT", + "Combined p-value" = "pG", + "Combined FDR" = "pGFdr", + "Combined Bonferroni p-values" = "pGFWER" + ) |> + dplyr::select( + all_of( + columns ) - write_tsv(res_reorder, snakemake@output[["table"]]) - sort_activated <- res_reorder[res_reorder$Status == "Activated", ] - sort_inhibited <- res_reorder[res_reorder$Status == "Inhibited", ] - write_tsv(sort_activated, snakemake@output[["table_activated"]]) - write_tsv(sort_inhibited, snakemake@output[["table_inhibited"]]) + ) |> + arrange( + desc(`total perturbation accumulation`) + ) + write_tsv(final_res, snakemake@output[["table"]]) } else { - columns <- c( - "Name", "Status", "Combined FDR", "total perturbation accumulation", - "number of genes on the pathway", "number of DE genes per pathway", - "p-value for at least NDE genes", "Combined Bonferroni p-values", - "p-value to observe a total accumulation", "Combined p-value", "Ids" - ) - emtpy_data_frame <- data.frame(matrix(nrow = 0, ncol = length(columns))) - colnames(emtpy_data_frame) <- columns + # the best hack for an empty tibble from a column specification I could find + emtpy_data_frame <- read_csv("\n", col_names = columns) write_tsv(emtpy_data_frame, snakemake@output[["table"]]) - write_tsv(emtpy_data_frame, snakemake@output[["table_activated"]]) - write_tsv(emtpy_data_frame, snakemake@output[["table_inhibited"]]) } -} +} \ No newline at end of file From a0da3284f38fe78aafcd7591ac8a5ef3e4a2c64f Mon Sep 17 00:00:00 2001 From: dlaehnemann Date: Thu, 16 Nov 2023 14:26:13 +0100 Subject: [PATCH 2/8] reduce spia.R indentation to two spaces per level --- workflow/scripts/spia.R | 122 ++++++++++++++++++++-------------------- 1 file changed, 61 insertions(+), 61 deletions(-) diff --git a/workflow/scripts/spia.R b/workflow/scripts/spia.R index a5b33289..9289d23f 100644 --- a/workflow/scripts/spia.R +++ b/workflow/scripts/spia.R @@ -48,69 +48,69 @@ if (nrow(sig_genes) == 0) { write_tsv(res, snakemake@output[["table_activated"]]) write_tsv(res, snakemake@output[["table_inhibited"]]) } else { - # get logFC equivalent (the sum of beta scores of covariates of interest) + # get logFC equivalent (the sum of beta scores of covariates of interest) - beta_col <- get_prefix_col("b", colnames(sig_genes)) + beta_col <- get_prefix_col("b", colnames(sig_genes)) - beta <- sig_genes |> - dplyr::select(ens_gene, !!beta_col) |> - deframe() + beta <- sig_genes |> + dplyr::select(ens_gene, !!beta_col) |> + deframe() - t <- tempdir(check = TRUE) - olddir <- getwd() - setwd(t) - prepareSPIA(db, pw_db) - res <- runSPIA( - de = beta, - all = universe, - pw_db, - plots = TRUE, - verbose = TRUE - ) - setwd(olddir) + t <- tempdir(check = TRUE) + olddir <- getwd() + setwd(t) + prepareSPIA(db, pw_db) + res <- runSPIA( + de = beta, + all = universe, + pw_db, + plots = TRUE, + verbose = TRUE + ) + setwd(olddir) - file.copy( - file.path(t, "SPIAPerturbationPlots.pdf"), - snakemake@output[["plots"]] - ) - pathway_names <- db[res$Name] - if (length(pathway_names) > 0) { - pathway_ids_tibble <- pathway_names@entries |> - map(slot, "id") |> - unlist() |> - as_tibble( - rownames="pathway_name" - ) |> - rename( - `pathway id` = value - ) - final_res <- as_tibble(res) |> - left_join( - pathway_ids_tibble, - join_by(Name == pathway_name) - ) |> - rename( - "number of genes on the pathway" = "pSize", - "number of DE genes per pathway" = "NDE", - "p-value for at least NDE genes" = "pNDE", - "total perturbation accumulation" = "tA", - "p-value to observe a total accumulation" = "pPERT", - "Combined p-value" = "pG", - "Combined FDR" = "pGFdr", - "Combined Bonferroni p-values" = "pGFWER" - ) |> - dplyr::select( - all_of( - columns - ) - ) |> - arrange( - desc(`total perturbation accumulation`) - ) - write_tsv(final_res, snakemake@output[["table"]]) - } else { - # the best hack for an empty tibble from a column specification I could find - emtpy_data_frame <- read_csv("\n", col_names = columns) - write_tsv(emtpy_data_frame, snakemake@output[["table"]]) - } + file.copy( + file.path(t, "SPIAPerturbationPlots.pdf"), + snakemake@output[["plots"]] + ) + pathway_names <- db[res$Name] + if (length(pathway_names) > 0) { + pathway_ids_tibble <- pathway_names@entries |> + map(slot, "id") |> + unlist() |> + as_tibble( + rownames="pathway_name" + ) |> + rename( + `pathway id` = value + ) + final_res <- as_tibble(res) |> + left_join( + pathway_ids_tibble, + join_by(Name == pathway_name) + ) |> + rename( + "number of genes on the pathway" = "pSize", + "number of DE genes per pathway" = "NDE", + "p-value for at least NDE genes" = "pNDE", + "total perturbation accumulation" = "tA", + "p-value to observe a total accumulation" = "pPERT", + "Combined p-value" = "pG", + "Combined FDR" = "pGFdr", + "Combined Bonferroni p-values" = "pGFWER" + ) |> + dplyr::select( + all_of( + columns + ) + ) |> + arrange( + desc(`total perturbation accumulation`) + ) + write_tsv(final_res, snakemake@output[["table"]]) + } else { + # the best hack for an empty tibble from a column specification I could find + emtpy_data_frame <- read_csv("\n", col_names = columns) + write_tsv(emtpy_data_frame, snakemake@output[["table"]]) + } } \ No newline at end of file From cd64c448ddd835ef917f7fa5ade8a603ed8c0719 Mon Sep 17 00:00:00 2001 From: dlaehnemann Date: Thu, 16 Nov 2023 14:28:54 +0100 Subject: [PATCH 3/8] remove activated and inhibited tables from spia reporting, as these are merely subsets of the main table without any further value added (contrary to previous variable naming, no sorting or anything happened in the creation of these tables) --- .../resources/datavzrd/spia-template.yaml | 110 +----------------- workflow/rules/datavzrd.smk | 4 - workflow/rules/enrichment.smk | 2 - 3 files changed, 1 insertion(+), 115 deletions(-) diff --git a/workflow/resources/datavzrd/spia-template.yaml b/workflow/resources/datavzrd/spia-template.yaml index fdac5d29..3b907ec2 100644 --- a/workflow/resources/datavzrd/spia-template.yaml +++ b/workflow/resources/datavzrd/spia-template.yaml @@ -70,112 +70,4 @@ views: 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 \ No newline at end of file + display-mode: hidden \ No newline at end of file diff --git a/workflow/rules/datavzrd.smk b/workflow/rules/datavzrd.smk index 51d3754d..a278a630 100644 --- a/workflow/rules/datavzrd.smk +++ b/workflow/rules/datavzrd.smk @@ -2,8 +2,6 @@ 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: @@ -53,8 +51,6 @@ 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}"), diff --git a/workflow/rules/enrichment.smk b/workflow/rules/enrichment.smk index 86890731..cb285c73 100644 --- a/workflow/rules/enrichment.smk +++ b/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, From a8d9b248d0f29178524aad29e98ece7c348f10b9 Mon Sep 17 00:00:00 2001 From: dlaehnemann Date: Thu, 16 Nov 2023 14:42:12 +0100 Subject: [PATCH 4/8] completely remove activated and inactivated tables from spia datavzrd template --- workflow/resources/datavzrd/spia-template.yaml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/workflow/resources/datavzrd/spia-template.yaml b/workflow/resources/datavzrd/spia-template.yaml index 3b907ec2..750d7ba5 100644 --- a/workflow/resources/datavzrd/spia-template.yaml +++ b/workflow/resources/datavzrd/spia-template.yaml @@ -4,14 +4,6 @@ datasets: 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: From 7110ffd6229c6c108a1e2cbf47bdf6db1bdfee20 Mon Sep 17 00:00:00 2001 From: dlaehnemann Date: Thu, 16 Nov 2023 14:42:58 +0100 Subject: [PATCH 5/8] update/correct spia.rst for correct column names --- workflow/report/spia.rst | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/workflow/report/spia.rst b/workflow/report/spia.rst index 9ed17445..bc6fca44 100644 --- a/workflow/report/spia.rst +++ b/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 `_): -``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 `_; 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. \ No newline at end of file From 4afecce4c74a21872f766e2db2a7ac0f5b42dbef Mon Sep 17 00:00:00 2001 From: dlaehnemann Date: Thu, 16 Nov 2023 14:43:26 +0100 Subject: [PATCH 6/8] bring in spia datavzrd template improvements from gfold workflow --- .../resources/datavzrd/spia-template.yaml | 45 ++++++++++--------- 1 file changed, 24 insertions(+), 21 deletions(-) diff --git a/workflow/resources/datavzrd/spia-template.yaml b/workflow/resources/datavzrd/spia-template.yaml index 750d7ba5..2bf55e60 100644 --- a/workflow/resources/datavzrd/spia-template.yaml +++ b/workflow/resources/datavzrd/spia-template.yaml @@ -1,4 +1,4 @@ -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 @@ -9,57 +9,60 @@ 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 \ No newline at end of file + pathway id: + display-mode: detail \ No newline at end of file From 1cc9477b0c3701a0f49ddf6e086a538208200214 Mon Sep 17 00:00:00 2001 From: dlaehnemann Date: Thu, 16 Nov 2023 15:40:31 +0100 Subject: [PATCH 7/8] include new required params: pathway_db: in spia datavzrd templating rule --- workflow/rules/datavzrd.smk | 2 ++ 1 file changed, 2 insertions(+) diff --git a/workflow/rules/datavzrd.smk b/workflow/rules/datavzrd.smk index a278a630..fd0edc83 100644 --- a/workflow/rules/datavzrd.smk +++ b/workflow/rules/datavzrd.smk @@ -6,6 +6,8 @@ rule render_datavzrd_config_spia: "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" From 553704089920f257335822035f5f5c54342d9f58 Mon Sep 17 00:00:00 2001 From: dlaehnemann Date: Thu, 16 Nov 2023 16:26:27 +0100 Subject: [PATCH 8/8] use latest version of datavzrd wrapper --- workflow/rules/datavzrd.smk | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflow/rules/datavzrd.smk b/workflow/rules/datavzrd.smk index fd0edc83..6cb123ce 100644 --- a/workflow/rules/datavzrd.smk +++ b/workflow/rules/datavzrd.smk @@ -65,7 +65,7 @@ rule spia_datavzrd: log: "logs/datavzrd-report/spia-{model}/spia-{model}.log", wrapper: - "v2.6.0/utils/datavzrd" + "v2.13.0/utils/datavzrd" rule diffexp_datavzrd: @@ -90,7 +90,7 @@ rule diffexp_datavzrd: log: "logs/datavzrd-report/diffexp.{model}/diffexp.{model}.log", wrapper: - "v2.6.0/utils/datavzrd" + "v2.13.0/utils/datavzrd" rule go_enrichment_datavzrd: @@ -117,4 +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" + "v2.13.0/utils/datavzrd"