PlotCHETAH: Plot the CHETAH classification on 2D visulization like t-SNE...

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

Description

Plot the CHETAH classification on 2D visulization like t-SNE + the corresponding classification tree, colored with the same colors

Usage

PlotCHETAH(input, redD = NA, interm = FALSE, return = FALSE,
  tree = TRUE, pt.size = 1, return_col = FALSE, col = NULL)

Arguments

input	a SingleCellExperiment on which CHETAHclassifier has been run
redD	the name of the reducedDim of the input to use for plotting
interm	color the intermediate instead of the final types
return	return the plot instead of printing it
tree	plot the tree, along with the classification
pt.size	the point-size of the classication plot
return_col	whether the colors that are used for the classification plot should be returned
col	custom colors for the cell types. the colors should be named with the corresponding cell types

Value

a ggplot object

Examples

## Standard plot (final types colored)
PlotCHETAH(input = input_mel)

## Intermediate types colored
PlotCHETAH(input = input_mel, interm = TRUE)

## Plot only the t-SNE plot
PlotCHETAH(input = input_mel, tree = FALSE)

jdekanter/CHETAH documentation built on Sept. 20, 2019, 3:31 a.m.