SingleR.PlotTsne: Plot a colored tSNE plot according to a set of labels

In dviraran/SingleR: Reference-based single-cell RNA-seq annotation

Description

Plot a colored tSNE plot according to a set of labels

Usage

SingleR.PlotTsne(SingleR, xy, labels = SingleR$labels, score.thres = 0,
  clusters = NULL, do.letters = TRUE, dot.size = 1,
  do.labels = FALSE, do.legend = TRUE, label.size = 3, title = "",
  colors = singler.colors, font.size = NULL, alpha = 0.5)

Arguments

SingleR	the output from the SingleR function
xy	a matrix with the coordinates of the single cells
labels	labels for the single cells, Default is the SingleR labels
score.thres	single-cells with a score lower than this number are marked as 'X'.
clusters	if the SingleR method is 'clusters' then this vector is the cluster id for each single cell
do.letters	if TRUE shows letters the first letter of the annotation
dot.size	the size of the dot. Default is 1
do.labels	only relevant in a 'cluster' method. If TRUE The cluster annotation is shown on top of the cluster.
do.legend	if TRUE legend is presented.
label.size	if do.labels is TRUE then this determines the font size of the labels
title	title for the plot
colors	colors to use
font.size	size of fonts in the plot
alpha	an alpha for the transparency of the dots

Value

a list with ggplot and a data frame with the coordinates and annotations

dviraran/SingleR documentation built on April 21, 2020, 3:23 p.m.