distribution_plots: per_unit_counts: Generates distribution plots of spot/cell...

In FridleyLab/spatialGE: Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression

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

Description

Generates violin plots, boxplots, or density plots of variables in the spatial meta data or of gene expression

Usage

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. If used in conjunction with plot_meta, the expression values are grouped using that variable
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). If plot_meta and gene are used together, then density plots are disabled
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. It also allows grouping of gene expression values by categorical variables (e.g., clusters).

FridleyLab/spatialGE documentation built on April 14, 2025, 9:37 a.m.