SingleDimPlot: Plot a single dimension

In satijalab/seurat: Tools for Single Cell Genomics

Plot a single dimension

Description

Plot a single dimension

Usage

SingleDimPlot(
  data,
  dims,
  col.by = NULL,
  cols = NULL,
  pt.size = NULL,
  shape.by = NULL,
  alpha = 1,
  alpha.by = NULL,
  order = NULL,
  label = FALSE,
  repel = FALSE,
  label.size = 4,
  cells.highlight = NULL,
  cols.highlight = "#DE2D26",
  sizes.highlight = 1,
  na.value = "grey50",
  raster = NULL,
  raster.dpi = NULL
)

Arguments

data	Data to plot
dims	A two-length numeric vector with dimensions to use
col.by	...
cols	Vector of colors, each color corresponds to an identity class. This may also be a single character or numeric value corresponding to a palette as specified by brewer.pal.info.By default, ggplot2 assigns colors
pt.size	Adjust point size for plotting
shape.by	If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells.
alpha	Alpha value for plotting (default is 1)
alpha.by	Mapping variable for the point alpha value
order	Specify the order of plotting for the idents. This can be useful for crowded plots if points of interest are being buried. Provide either a full list of valid idents or a subset to be plotted last (on top).
label	Whether to label the clusters
repel	Repel labels
label.size	Sets size of labels
cells.highlight	A list of character or numeric vectors of cells to highlight. If only one group of cells desired, can simply pass a vector instead of a list. If set, colors selected cells to the color(s) in cols.highlight and other cells black (white if dark.theme = TRUE); will also resize to the size(s) passed to sizes.highlight
cols.highlight	A vector of colors to highlight the cells as; will repeat to the length groups in cells.highlight
sizes.highlight	Size of highlighted cells; will repeat to the length groups in cells.highlight
na.value	Color value for NA points when using custom scale.
raster	Convert points to raster format, default is NULL which will automatically use raster if the number of points plotted is greater than 100,000
raster.dpi	the pixel resolution for rastered plots, passed to geom_scattermore(). Default is c(512, 512)

Value

A ggplot2 object

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.