spatial_signature_plot: Plot spatial expression

In Czh3/iSpatial: infer transcriptome-wide spatial expression via integration of scRNA and spRNA

Plot spatial expression

Description

Plot the spatial expression patterns on a group of genes.

Usage

spatial_signature_plot(
  object,
  assay = "enhanced",
  gene.set,
  set.name,
  pt.size.factor = 2,
  alpha = 0.5,
  color.scale = c("gray95", "gray80", "wheat", "pink", "orange", "red", "red4"),
  quantile.cutoff = 0.95,
  legend = FALSE
)

Arguments

object	seurat object
assay	choose assay
gene.set	vector contain the genes to plot
set.name	set the name for the plot
pt.size.factor	point size
alpha	transparency of the points
color.scale	set the color scale. Default: c("gray95", "gray80", "pink", "orange", "red", "red4")
quantile.cutoff	0 to 1. Set the quantile of expression of the max value. Default: 0.95% of the max.
legend	whether to plot the legend

Value

ggplot object

Czh3/iSpatial documentation built on Sept. 15, 2022, 10:32 p.m.