Commit 45bd2866 authored by Lena Hersemann's avatar Lena Hersemann

removed error message (missing pathways) as it interfered with knitter

parent 9fbb9fb8
......@@ -354,7 +354,6 @@ session::save.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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