spatialFeaturePlot: A spatial feature plots

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

A spatial feature plots

Description

This function takes a CellChat object as input, and then plot gene expression distribution over spots/cells on the image.

Usage

spatialFeaturePlot(
  object,
  features = NULL,
  signaling = NULL,
  pairLR.use = NULL,
  enriched.only = TRUE,
  thresh = 0.05,
  do.group = TRUE,
  color.heatmap = "Spectral",
  n.colors = 8,
  direction = -1,
  do.binary = FALSE,
  cutoff = NULL,
  color.use = NULL,
  alpha = 1,
  point.size = 0.8,
  legend.size = 3,
  legend.text.size = 8,
  shape.by = 16,
  ncol = NULL,
  show.legend = TRUE,
  show.legend.combined = FALSE
)

Arguments

object	cellchat object
features	a char vector containing features to visualize. 'features' can be genes or column names of 'object@meta'.
signaling	signalling names to visualize
pairLR.use	a data frame consisting of one column named "interaction_name", defining the L-R pairs of interest
enriched.only	whether only return the identified enriched signaling genes in the database. Default = TRUE, returning the significantly enriched signaling interactions
thresh	threshold of the p-value for determining significant interaction when visualizing links at the level of ligands/receptors;
do.group	set 'do.group = TRUE' when only showing enriched signaling based on cell group-level communication; set 'do.group = FALSE' when only showing enriched signaling based on individual cell-level communication
color.heatmap	A character string or vector indicating the colormap option to use. It can be the avaibale color palette in brewer.pal() or viridis_pal() (e.g., "Spectral","viridis")
n.colors, direction	n.colors: number of basic colors to generate from color palette; direction: Sets the order of colors in the scale. If 1, the default colors are used. If -1, the order of colors is reversed.
do.binary, cutoff	whether binarizing the expression using a given cutoff
color.use	defining the color for cells/spots expressing ligand only, expressing receptor only, expressing both ligand & receptor and cells/spots without expression of given ligands and receptors
alpha	the transparency of individual spot
point.size	the size of cell slot
legend.size	the size of legend
legend.text.size	the text size on the legend
shape.by	the shape of individual spot
ncol	number of columns if plotting multiple plots
show.legend	whether show each figure legend
show.legend.combined	whether show the figure legend for the last plot

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