There is a name conflict between the actual pipeline and the util: .plot_heatmap_and_write_genes is called in pipeline (See here) while it was implemented as plot_heatmap_and_write_genes without the first dot (See here).
Furthermore, pheatmap was directly called inside .plot_heatmap_and_write_genes thus exposing the figure object to console. If saving the figure by using pdf() and dev.off(), there would always exists an empty page. Using filename parameter of pheatmap is highly suggested.
(Excuse me that trailing spaces are removed by my IDE, which might lead to distraction when you are reviewing my PR).
There is a name conflict between the actual pipeline and the util:
.plot_heatmap_and_write_genesis called in pipeline (See here) while it was implemented asplot_heatmap_and_write_geneswithout the first dot (See here).Furthermore,
pheatmapwas directly called inside.plot_heatmap_and_write_genesthus exposing the figure object to console. If saving the figure by usingpdf()anddev.off(), there would always exists an empty page. Usingfilenameparameter ofpheatmapis highly suggested.(Excuse me that trailing spaces are removed by my IDE, which might lead to distraction when you are reviewing my PR).