spatialDimPlot: Visualize spatial cell groups

In sqjin/CellChat: Inference and analysis of cell-cell communication from single-cell and spatial transcriptomics data

Visualize spatial cell groups

Description

This function takes a CellChat object as input, and then plot cell groups of interest.

Usage

spatialDimPlot(
  object,
  color.use = NULL,
  group.by = NULL,
  sources.use = NULL,
  targets.use = NULL,
  idents.use = NULL,
  alpha = 1,
  shape.by = 16,
  title.name = NULL,
  point.size = 2.4,
  legend.size = 5,
  legend.text.size = 8,
  legend.position = "right",
  ncol = 1,
  byrow = FALSE
)

Arguments

object	cellchat object
color.use	defining the color for each cell group
group.by	Name of one metadata columns to group (color) cells. Default is the defined cell groups in CellChat object
sources.use	a vector giving the index or the name of source cell groups
targets.use	a vector giving the index or the name of target cell groups
idents.use	a vector giving the index or the name of cell groups of interest
alpha	the transparency of individual spot
shape.by	the shape of individual spot
title.name	title name
point.size	the size of spots
legend.size	the size of legend
legend.text.size	the text size on the legend
legend.position	legend position
ncol	number of columns of the legend text
byrow	arrange the legend text byrow or not

sqjin/CellChat documentation built on Nov. 10, 2023, 4:29 a.m.