Dear smorabit, thank you for implementing this very useful tool! I managed to run hdWGCNA successfully on my dataset, and results seem in line with my expectations. Now I am dealing with the visualization bit, particularly with the ModuleFeaturePlot function.
I was wondering what is the reason for choosing a symmetric gradient range (restrict_range = TRUE) when plotting hMEs (features = "hMEs"). I noticed that in some of my modules the resulting visualizations are a lot different to each others, therefore allowing for kind of different interpretations of plots. Of course this is particularly evident when the hME limits for a given module are skewed towards positive/negative values (as in this case the symmetric range would "balance" the skewed values around 0).
As an example, see below the hME values of the green module when restrict_range = TRUE
and when restrict_range = FALSE (here, I have also plotted raw hME values for reference)
I understand it is just a matter of visualization maybe, but in the second case it'd be way easier to convince someone that the green module is specific to the cell clusters on the bottom.
Thank you for helpin!
Dear smorabit, thank you for implementing this very useful tool! I managed to run hdWGCNA successfully on my dataset, and results seem in line with my expectations. Now I am dealing with the visualization bit, particularly with the ModuleFeaturePlot function.
I was wondering what is the reason for choosing a symmetric gradient range (
restrict_range = TRUE) when plotting hMEs (features = "hMEs"). I noticed that in some of my modules the resulting visualizations are a lot different to each others, therefore allowing for kind of different interpretations of plots. Of course this is particularly evident when the hME limits for a given module are skewed towards positive/negative values (as in this case the symmetric range would "balance" the skewed values around 0).As an example, see below the hME values of the green module when
restrict_range = TRUEand when
restrict_range = FALSE(here, I have also plotted raw hME values for reference)I understand it is just a matter of visualization maybe, but in the second case it'd be way easier to convince someone that the green module is specific to the cell clusters on the bottom.
Thank you for helpin!