plot_gene: Plot on a gene or gene

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

Description

This will plot gene information onto a 2d plot

Usage

plot_gene(
  input,
  gene,
  facet_by = NULL,
  assay = NULL,
  coords = NULL,
  title = NULL,
  colors = c("gray", "blue", "red", "yellow"),
  size = 1.5,
  ncol = 2,
  text_sizes = c(20, 10, 5, 10, 5, 5),
  xlab = "x",
  ylab = "y"
)

Arguments

input	The input data
gene	the gene or genes to plot
facet_by	If ONE gene is being plotted it can be faceted. You cannot facet multiple gene
assay	The assay to operate on. Will default to get_def_assay(input)
coords	A vector of character lem, x, and u. See set_xy function.
title	The title
colors	Colors for the cells
size	The size of the points
ncol	controls the number of columns if faceting
text_sizes	the text sizes on the plot
xlab	character x label
ylab	character y label
theme	the ggplot theme

Details

Utilize information stored in colData to control the plot display.

Examples

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

kgellatl/SignalCell documentation built on Sept. 3, 2020, 8:45 a.m.