PlotTSNE: Plots a variable on a t-SNE

Description Usage Arguments Value Examples

Description

Plots a variable on a t-SNE

Usage

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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

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

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