plot_st_gene: Plot spatial distribution of gene

In ZJUFanLab/SpaTalk: Infer Cell-Cell Communication for Spatial Transcriptomics

Plot spatial distribution of gene

Description

Point plot with spatial distribution of a gene for transcriptomics data

Usage

plot_st_gene(
  object,
  gene,
  size = 1,
  color_low = "grey",
  color_mid = NULL,
  color_high = "blue",
  color_midpoint = NULL,
  if_use_newmeta = T,
  celltype = NULL,
  if_plot_others = T
)

Arguments

object	SpaTalk object generated from dec_celltype.
gene	Symbol of gene, e.g., 'AKT1'.
size	Point size. Default is 1.
color_low	Color for the lowest value.
color_mid	Color for the middle value for using scale_color_gradient2. Default is NULL.
color_high	Color for the highest value.
color_midpoint	Value for the middle scale. Default is NULL.
if_use_newmeta	Whether to use newmeta o plot the spatial distribution of gene after dec_celltype for spot-based data. Default is TRUE.
celltype	gene in which celltype to plot. Default is NULL. Set if_use_newmeta TRUE when using this parameter.
if_plot_others	Whether to plot other cells when to use defined celltype.

Details

Please set if_use_newmeta as FALSE to plot the spatial distribution of gene before dec_celltype for spot-based data.

ZJUFanLab/SpaTalk documentation built on Jan. 21, 2025, 3:13 p.m.