per_unit_counts: Generates distribution plots of spot/cell meta data or gene expression

Generates violin plots, boxplots, or density plots of continuous variables in the spatial meta data or of gene expression to make comparisons across samples

distribution_plots(
  x = NULL,
  plot_meta = NULL,
  genes = NULL,
  samples = NULL,
  data_type = "tr",
  color_pal = "okabeito",
  plot_type = "violin",
  ptsize = 0.5,
  ptalpha = 0.5
)

Arguments

x

an STlist

plot_meta

vector of variables in x@spatial_meta to plot distributions. If 'total_counts', the function plots the counts per spot/cell. If 'total_genes', the function plots the number of genes per spot/cell are plotted.

genes

vector of genes to plot expression distribution

samples

samples to include in the plot. Default (NULL) includes all samples

data_type

one of 'tr' or 'raw', to plot transformed or raw counts

color_pal

a string of a color palette from khroma or RColorBrewer, or a vector with colors

plot_type

one of "violin", "box", or "density" (violin plots, box plots, or density plots respectively)

ptsize

the size of points in the plots

ptalpha

the transparency of points (violin/box plot) or curves (density plots)

Details

The function allows to visualize the distribution of spot/cell total counts, total genes, or expression of specific genes across all samples for comparative purposes.