PlotExprCODEXemb: Plot expression of a gene or protein in the CODEX UMAP or...
In CamaraLab/STvEA: Spatially-resolved Transcriptomics via Epitope Anchoring

PlotExprCODEXemb

R Documentation

Plot expression of a gene or protein in the CODEX UMAP or t-SNE embedding

Description

Plot expression of a gene or protein in the CODEX UMAP or t-SNE embedding

Usage

PlotExprCODEXemb(
  stvea_object,
  name,
  type = "protein",
  high_color = "red",
  high_color2 = "green",
  low_color = "light gray",
  pt_size = 0.8
)

Arguments

`stvea_object`	STvEA.data class with CODEX expression and embedding
`name`	gene or protein name to plot
`type`	which type of expression data should be plotted? "RNA" or "protein"
`high_color`	color of high expression on the color ramp
`high_color2`	color of high expression for the second protein or gene, if provided
`low_color`	color of low/no expression on the color ramp
`pt_size`	ggplot geom_point size