use metadata (or active ident) in plot_stat

[williamsdrake]

Thanks for your useful project. When using plot_stat, I've noticed that the stacked barplot is fixed to the 'seurat_clusters' in the metadata. Would it be possible for an additional argument to be added so that we can use other metadata to label the stacked barplot?

Referring to these lines:

Scillus/R/visualization.R

Line 392 in 4e7884d

cluster = dataset[['seurat_clusters']][[1]])

Scillus/R/visualization.R

Line 400 in 4e7884d

length(unique(dataset[['seurat_clusters']][[1]]))

[williamsdrake]

Got impatient so I modified the relevant code adding a 'clusterLabel' argument which defaults to "seurat_clusters". Would be nice if you added it to the project. Here it is:

plot_stat <- function(dataset, 
                      plot_type, 
                      clusterLabel = "seurat_clusters",
                      group_by = "sample",
                      pal_setup = 'Set2',
                      plot_ratio = 1,
                      text_size = 10,
                      tilt_text = FALSE) {
  
  if (is.data.frame(pal_setup)) {
    pal <- pal_setup[pal_setup[[1]] == group_by,][[2]]
  } else {
    pal <- pal_setup
  }
  
  stat <- tibble::tibble(group = dataset[[group_by]][[1]], 
                         cluster = dataset[[clusterLabel]][[1]])
  stat %<>%
    group_by(.data$group, 
             .data$cluster) %>%
    summarise(n = n()) %>%
    mutate(freq = n / sum(n))
  
  ncolors <- if (plot_type == 'prop_fill') {
    length(unique(dataset[[clusterLabel]][[1]]))
  } else {
    length(unique(dataset[[group_by]][[1]]))
  }

[iddryg]

Agreed, I came here to mention this. I'd previously labeled my clusters with the RenameIdents() function in Seurat, and using Scillus am unable to get it to plot with those renamed idents. It only plots the cluster numbers.

I got around this by just writing my Idents to the 'seurat_clusters' metadata column, but a more customizable way like suggested above would be nice.