Are the barplots applicable to expression features split by groupings/condition? about sccustomize HOT 3 CLOSED

Hi @levinhein

thanks for nice words! Just wanted to let you know I’m currently on paternity leave and will get back to your issue when I return July 25th. Sorry for delay!

Thanks,
Sam

from sccustomize.

Hi @samuel-marsh! Thanks for the heads up! I'm a big fan of your computational works! And congrats, sending my wishes of best health and happiness for baby Evan! :)) (updated from Twitter ff you :)

from sccustomize.

Hi,

Sorry it's taken me so long to get back to this! So in short yes you could do this kind of visualization for genes or module scores but to me I don't think it's great representation of the data. When plotting those kind of things the distribution of scores or expression is critically important and that gets lost when you simply take medians and plot in this way. I think violin plots make a more informative plot for that reason.

That said if you want to try it out and make the plots you definitely can. You just need to pull data and create a by sample dataframe that also contains a grouping factor column. The actual plotting code is pretty straightforward:

library(ggplot2)
library(scCustomize) # for theme_ggprism_mod

plot <- ggplot(data = merged, mapping = aes(x = GROUP_NAME, y = FEATURE, fill = GROUP_NAME)) +
      geom_boxplot(fill = "white") +
      geom_dotplot(binaxis ='y', stackdir = 'center') +
      scale_fill_manual(values = colors_use) +
      theme_ggprism_mod() +
      ggtitle(plot_title) +
      ylab(y_axis_label) +
      xlab("")

Best,
Sam

from sccustomize.