Thanks a lot for the nice package, which sees higher usage frequency in our lab (Bodenmiller).
For downstream visualization, I have some notes/questions regarding your signifPlot and topPairs functions.
1. Heatmap via signifPlot
A) Would be helpful if there would be some explanation in the function help page / vignette on what exactly is displayed - Looking into the source code it looks like it is the (-)log10(p.value/FDR) depending on whether the coefficient is positive or negative, correct?
B) As with the “bubble” plot, it would be helpful if "significant" results would be marked (e.g. or all other tiles set to 0).
C) A data_out option would be cool to allow compatibility with other visualization packages (e.g. ComplexHeatmap) - Potentially relevant for both plotting options.
D) Currently any character vector (such as “random_word”) would create the heatmap - Potentially worthwhile to specify the exact options.
2. topPairs
A) The cutoff option does not seem to actually select the appropriate rows.
I am using spicyR_1.14.2 (lisaClust 1.10.1). If any of these points were addressed in newer releases/devel, my apologies.
Hi spicyR team,
Thanks a lot for the nice package, which sees higher usage frequency in our lab (Bodenmiller).
For downstream visualization, I have some notes/questions regarding your
signifPlotandtopPairsfunctions.1. Heatmap via
signifPlotA) Would be helpful if there would be some explanation in the function help page / vignette on what exactly is displayed - Looking into the source code it looks like it is the (-)log10(p.value/FDR) depending on whether the coefficient is positive or negative, correct?
B) As with the “bubble” plot, it would be helpful if "significant" results would be marked (e.g. or all other tiles set to 0).
C) A
data_outoption would be cool to allow compatibility with other visualization packages (e.g.ComplexHeatmap) - Potentially relevant for both plotting options.D) Currently any character vector (such as “random_word”) would create the heatmap - Potentially worthwhile to specify the exact options.
2. topPairs
A) The cutoff option does not seem to actually select the appropriate rows.
I am using spicyR_1.14.2 (lisaClust 1.10.1). If any of these points were addressed in newer releases/devel, my apologies.
Thanks in advance! Best, Lasse