dotPlot: Dot plot

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

Dot plot

Description

The size of the dot encodes the percentage of cells within a class, while the color encodes the AverageExpression level across all cells within a class

Usage

dotPlot(
  object,
  features,
  rotation = TRUE,
  colormap = "OrRd",
  color.direction = 1,
  color.use = c("#F8766D", "#00BFC4"),
  scale = TRUE,
  col.min = -2.5,
  col.max = 2.5,
  dot.scale = 6,
  assay = "RNA",
  idents = NULL,
  group.by = NULL,
  split.by = NULL,
  legend.width = 0.5,
  angle.x = 45,
  hjust.x = 1,
  angle.y = 0,
  hjust.y = 0.5,
  show.legend = TRUE,
  ...
)

Arguments

object	seurat object
features	Features to plot (gene expression, metrics)
rotation	whether rotate the plot
colormap	RColorbrewer palette to use (check available palette using RColorBrewer::display.brewer.all()). default will use customed color palette
color.direction	Sets the order of colours in the scale. If 1, the default, colours are as output by RColorBrewer::brewer.pal(). If -1, the order of colours is reversed.
color.use	defining the color for each condition/dataset
scale	whther show x-axis text
col.min	Minimum scaled average expression threshold (everything smaller will be set to this)
col.max	Maximum scaled average expression threshold (everything larger will be set to this)
dot.scale	Scale the size of the points, similar to cex
assay	Name of assay to use, defaults to the active assay
idents	Which classes to include in the plot (default is all)
group.by	Name of one or more metadata columns to group (color) cells by (for example, orig.ident); pass 'ident' to group by identity class
split.by	Name of a metadata column to split plot by;
legend.width	legend width
angle.x	angle for x-axis text rotation
hjust.x	adjust x axis text
angle.y	angle for y-axis text rotation
hjust.y	adjust y axis text
show.legend	whether show the legend
...	Extra parameters passed to DotPlot from Seurat package

Value

ggplot2 object

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