transpose = T/F in make.pheatmap() produced inconsistent results

[denvercal1234GitHub]

Hi there,

Thank you for the package.

When I plotted the same data and markers but with transpose=T or transpose = F, the expression for markers per cluster were different. For example, cluster 5 showed much more expression for more markers compared to that shown for cluster 5 when transpose = T.

Would you mind helping me clarify potential source of this inconsistency?

Note I used only a few markers in run.flowsom(), but I set use.cols in make.pheatmap and do.aggregate = to all cellular markers because I want to visualize the median expression of all markers and not only markers that were used in the clustering.

Thank you again.

exp_all_cellular.cols <- do.aggregate(F33_data.list_cell.dat_runflowsom_cellular.cols, use.cols=all_cellular.cols, by = "FlowSOM_metacluster")

make.pheatmap(exp_all_cellular.cols, "FlowSOM_metacluster", plot.cols = all_cellular.cols, transpose = F)

make.pheatmap(exp_all_cellular.cols, "FlowSOM_metacluster", plot.cols = all_cellular.cols, transpose = T)