dotPlot: 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,
  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.

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