Commit 9fbb9fb8 authored by Lena Hersemann's avatar Lena Hersemann

removed `/` when part of the contrast label; adjusted error message for missing pathway data

parent 1fa78d9e
......@@ -324,12 +324,14 @@ term_barplot_files = erPlotData %>% do({
# scale_y_log10()
## todo use builtin method to create filesystem-compatible name
label <- gsub('[^a-zA-Z0-9.!=><&|]', '_', label)
fileNameLabel <- label %>%
str_replace_all("!=", "ne") %>%
str_replace_all(">", "gt") %>%
str_replace_all("<", "lt") %>%
str_replace_all(fixed("&"), "AND") %>%
str_replace_all(fixed("|"), "OR") %>%
str_replace_all(fixed("/"), "_") %>%
str_replace_all(" ", "_")
# ggsave(paste0("enrichmed_terms__", fileNameLabel, ".pdf"))
......@@ -348,11 +350,11 @@ walk(term_barplot_files$file, function(pngFile){ cat(paste0("<img src='", pngFil
session::save.session(".cp_enrichment.dat");
# session::restore.session(".cp_enrichment.dat");
########################################################################################################################
#' ## Enriched KEGG Pathways
#' To understand spatio-temporal changes in gene expression better we now overlay enriched kegg pathways with the -log10(q_value) of each contrast. The direction of the expression changes is encoded as color, whereby red indicates that sample_1 is overexpressed. Because we have multiple contrasts of interest, this defines a slice-color barcode for each gene. To relate the barcode to contrasts we define the following slice order:
if(is.null(opts$overlay_expr_data)) stop("stopping here because we dont have pathway data")
hasEnrPathways=(!is.null(opts$overlay_expr_data) & (nrow(enrResults %>% filter(ontology=="kegg")) >0))
#+ eval=hasEnrPathways
......
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