perf bump datavzrd wrapper to 2.6.0 and general bug fixes

snakemake-workflows · Aug 28, 2023 · bd964f7 · bd964f7
1 parent 96c9747
commit bd964f7
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Showing 3 changed files with 6 additions and 8 deletions.
diff --git a/workflow/rules/datavzrd.smk b/workflow/rules/datavzrd.smk
@@ -67,8 +67,7 @@ rule spia_datavzrd:
  log:
  "logs/datavzrd-report/spia-{model}/spia-{model}.log",
  wrapper:
- "v1.29.0/utils/datavzrd"
-
+ "v2.6.0/utils/datavzrd"
 
 rule diffexp_datavzrd:
  input:
@@ -92,7 +91,7 @@ rule diffexp_datavzrd:
  log:
  "logs/datavzrd-report/diffexp.{model}/diffexp.{model}.log",
  wrapper:
- "v1.29.0/utils/datavzrd"
+ "v2.6.0/utils/datavzrd"
 
 
 rule go_enrichment_datavzrd:
@@ -119,4 +118,4 @@ rule go_enrichment_datavzrd:
  log:
  "logs/datavzrd-report/go_enrichment-{model}/go_enrichment-{model}_{gene_fdr}.go_term_fdr_{go_term_fdr}.log",
  wrapper:
-  "v1.29.0/utils/datavzrd"
+ "v2.6.0/utils/datavzrd"
diff --git a/workflow/scripts/plot_diffexp_heatmap.R b/workflow/scripts/plot_diffexp_heatmap.R
@@ -53,7 +53,7 @@ if (all(selectedgenes == 0)) {
  # If number of transcripts is more than 100,
  # Since for RNA-seq multiple transcripts may present for a single gene.
 } else if (nrow(selectedgenes) > 100) {
- pdf_height <- round(nrow(selectedgenes) / 7)
+ pdf_height <- round(nrow(selectedgenes) / 5)
  pdf(snakemake@output[["diffexp_heatmap"]],
  height = pdf_height, width = ncol(selectedgenes) * 2
  )
@@ -63,7 +63,7 @@ if (all(selectedgenes == 0)) {
  )
  dev.off()
 } else {
- pdf_height <- round(nrow(selectedgenes) / 7)
+ pdf_height <- round(nrow(selectedgenes) / 5)
  pdf(
  file = snakemake@output[["diffexp_heatmap"]],
  height = pdf_height, width = ncol(selectedgenes) * 2

diff --git a/workflow/scripts/spia.R b/workflow/scripts/spia.R
@@ -21,7 +21,6 @@ diffexp <- read_tsv(snakemake@input[["diffexp"]]) %>%
  mutate(ens_gene = str_c("ENSEMBL:", ens_gene))
 universe <- diffexp %>% pull(var = ens_gene)
 sig_genes <- diffexp %>% filter(qval <= 0.05)
-
 if (nrow(sig_genes) == 0) {
  cols <- c(
  "Name", "Status", "Combined FDR",
@@ -30,7 +29,7 @@ if (nrow(sig_genes) == 0) {
  "Combined Bonferroni p-values",
  "p-value to observe a total accumulation", "Combined p-value", "Ids"
  )
- res <- data.frame(matrix(ncol = 7, nrow = 0, dimnames = list(NULL, cols)))
+ 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"]])