PlotCHETAH {CHETAH} | R Documentation

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

### 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)

[Package CHETAH version 1.3.0 Index]