pointDRPlot: pointDRPlot

In wguo-research/scCancer: A package for automated processing of single cell RNA-seq data in cancer

pointDRPlot

Description

Plot scatter for cells.

Usage

pointDRPlot(
  cell.annotation,
  value,
  sel.clusters = NULL,
  coor.names = c("tSNE_1", "tSNE_2"),
  colors = NULL,
  discrete = T,
  limit.quantile = 0,
  point.type = 1,
  legend.position = "right",
  legend.title = NULL
)

Arguments

cell.annotation	A data.frame of cells' annotation containing the cells' coordinates and index to be colored.
value	The column name of cell.annotation, which is mapped to the colors of points.
sel.clusters	An array of selected clusters to present. (The default is NULL and all clusters will be used.)
coor.names	A vector indicating the names of two-dimension coordinate used in visualization.
colors	An array of colors used to show the gredients or type of points. If NULL, the default colors will be used.
discrete	A logical value indicating whether the value column is discrete or not.
limit.quantile	A quantile threshold to limit the data and reduce the influence of outliers.
point.type	A number indicating the shape type of points. "1" (default) means the point has a lightgrey border, and "2" means not.
legend.position	The position of legends ("none", "left", "right", "bottom", "top", or two-element numeric vector).
legend.title	The title of legends.

Value

A ggplot object for the scatter plot.

wguo-research/scCancer documentation built on May 26, 2024, 9:12 p.m.