PlotTSNE: Plots a variable on a t-SNE

In CHETAH: Fast and accurate scRNA-seq cell type identification

Description

Plots a variable on a t-SNE

Usage

PlotTSNE(toplot, input, redD = NA, col = NULL, return = FALSE,
  limits = NULL, pt.size = 1, shiny = NULL, y_limits = NULL,
  x_limits = NULL, legend_label = "")

Arguments

toplot	the variable that should be plotted. Either a character vector or a factor, or a (continuous) numeric. If toplot is not named with the rownames of redD, it is assumed that the order of the two is the same.
input	a SingleCellExperiment on which CHETAHclassifier has been run
redD	the name of the reducedDim of the input to use for plotting
col	a vector of colors. If toplot is a numeric, this will become a continuous scale. If toplot is a charachter vector, the colors should be named with the unique values (/levels) of toplot
return	instead of printing, return the ggplot object
limits	the limits of the continuous variable to plot. When not provided the minimal and maximal value will be used
pt.size	the point-size
shiny	Needed for the shiny application: should always be NULL
y_limits	the y-axis limits
x_limits	the x-axis limits, if NULL
legend_label	the label of the legend

Value

A ggplot object

Examples

CD8 <- assay(input_mel)['CD8A', ]
PlotTSNE(toplot = CD8, input = input_mel)

CHETAH documentation built on Nov. 8, 2020, 8:02 p.m.