compare_SThet: compare_SThet: Compares spatial autocorrelation statistics...

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

compare_SThet: Compares spatial autocorrelation statistics across samples

Description

Plots the spatial autocorrelation statistics of genes across samples and colors samples acording to sample metadata.

Usage

compare_SThet(
  x = NULL,
  samplemeta = NULL,
  genes = NULL,
  color_by = NULL,
  categorical = T,
  color_pal = "muted",
  ptsize = 1
)

Arguments

x	an STlist.
samplemeta	a string indicating the name of the variable in the clinical data frame. If NULL, uses sample names
genes	the name(s) of the gene(s) to plot.
color_by	the variable in x@spatial_meta used to color points in the plot. If NULL, each sample is assigned a different color
categorical	logical indicating whether or not to treat color_by as a categorical variable. Default is TRUE
color_pal	a string of a color palette from khroma or RColorBrewer, or a vector with colors with enough elements to plot categories.
ptsize	a number specifying the size of the points. Passed to the size aesthetic.

Details

This function takes the names of genes and their Moran's I or Geary's C computed for multiple samples and to provide a muti-sample comparison. Samples in the plot can be colored according to sample metadata to explore potential associations between spatial distribution of gene expression and sample-level data.

Value

a list of plots

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