Fixed pval format in report, added test

qbic-pipelines · Nov 20, 2024 · 5f23f54 · 5f23f54
1 parent 02fc8ff
commit 5f23f54
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 1 deletion.
diff --git a/assets/RNAseq_report.Rmd b/assets/RNAseq_report.Rmd
@@ -2058,7 +2058,7 @@ if (!isProvided(params$datasources)) {
 # Set default params
 # ------------------
 pathway_pval_threshold <- ifelse(params$pathway_pval_threshold == -1, params$adj_pval_threshold, params$pathway_pval_threshold)
-pathway_pval_text <- as.character(pathway_pval_threshold)
+pathway_pval_text <- format(pathway_pval_threshold, scientific=F)
 
 # Set theme for graphs
 theme_set(theme_classic())

diff --git a/conf/test.config b/conf/test.config
@@ -28,6 +28,7 @@ params {
     software_versions = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/software_versions.csv'
     multiqc = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/MultiQC.zip'
     run_pathway_analysis = true
+    pathway_pval_threshold = 0.0003
     datasources = 'KEGG,REAC'
     genome = 'GRCm38'
     quote = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/offer_example.pdf'