plotting the expression profiles of different conditions in same plot

Question

[Za]

Hi

I have four gene expression profiles for 4 different conditions with different list of genes, how I can show a heat map of these genes while I don't want to take intersection of 4 lists rather I want to show 4 lists in one heat map?

[cpad0112]

you can annotate the heatmap for 4 different conditions.

[Za]

Sorry how??? If I merge 4 conditions in one matrix, some genes would be NA because I need all genes not common ones among 4 conditions

[cpad0112]

Do these 4 conditions share same set of genes? i.e let us say under 4 conditions, you would like to show expression profiles of 50 genes of interest? or 4 different conditions share few genes, rest of them unique to each condition?

[Za]

Thanks a lot

"4 different conditions share few genes, rest of them unique to each condition" and I am interested in all genes not common ones but in one heat map or other sort of plots showing expression levels

[cpad0112]

I am not sure if heatmap is an ideal way of showing non-common genes for 4 different conditions. You may consider dotplots from clusterprofiler package. https://bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html. Please look in dotplot section. You can also facet with upregulation and downregulation. On x axis you can plot conditions and on y axis gene names. Representation can be done either for p-value or for fc. You can also consider upset plots (upsetter package in R)

It would be helpful if you could post some representative data for 4 conditions.

[Chirag Parsania]

ComplexHeatmap might help.