plot_tsne_gene: tSNE Plot on a gene or gene

In kgellatl/SignallingSingleCell: Network Analysis for single cell RNA sequencing Data (sc-RNASeq)

Description

This will plot gene information onto a 2d tsne plot

Usage

plot_tsne_gene(
  input,
  gene,
  log_scale = F,
  title = "",
  density = FALSE,
  facet_by = "NA",
  colors_points = c("gray", "blue", "red", "yellow"),
  size = 1.5,
  ncol = 2,
  resolution = 250,
  theme = "classic",
  cutoff = 0.2,
  xcol = "x",
  ycol = "y",
  text_sizes = c(20, 10, 5, 10, 5, 5),
  density_scale = 1,
  background_sample = F
)

Arguments

input	The input data
gene	the gene or gene to ploy
log_scale	if true will log2(value)
title	The title
density	If true will color a density of the points
facet_by	If ONE gene is being plotted it can be faceted. You cannot facet multiple gene
colors_points	Colors for the cells
size	The size of the points
ncol	controls the number of columns if faceting
resolution	Control the density drawing resolution. Higher values will increase file size
cutoff	removes points from density below this threshold. Lower values will increase file size
xcol	pData column to use for x axis
ycol	pData column to use for y axis

Details

Utilize information stored in pData to control the plot display.

Examples

plot_tsne_gene(ex_sc_example, gene = "Tnf", title = "Tnf over Time", facet_by = "Timepoint", density = TRUE)

kgellatl/SignallingSingleCell documentation built on Dec. 29, 2021, 4:12 p.m.