set up a data.frame for barplot visualization for a gene

set up a data.frame for barplot visualization for a gene

simba_barplot_df(sce, genesym, colvars = "celltype")

Arguments

sce

SingleCellExperiment with altExp element "sprobs"

genesym

character(1)

colvars

character() columns from colData(sce) to propagate

Value

data.frame with elements rank, prob, and propagated columns

Examples

data(nn50)
data(t3k)
t3k = add_simba_scores(nn50, t3k)
gns = c("CST3", "MS4A1", "NKG7", "GAPDH")
alldf = lapply(gns, function(x) simba_barplot_df(t3k, x, 
  colvars = "celltype"))
alldf = do.call(rbind, alldf)
ggplot(alldf, aes(x=rank,xend=rank,y=0, yend=prob,colour=celltype)) + geom_point() +
  geom_segment() + facet_wrap(~symbol, ncol=2) + 
    theme(strip.text=element_text(size=24), 
      legend.text=element_text(size=24), 
      axis.text=element_text(size=24)) +
    guides(colour = guide_legend(override.aes = 
       list(linetype=1, lwd=2)))