plotMarkers: Plot gene expression patterns

In minzheguo/SINCERA: An R implementation of SINCERA pipeline for processing single-cell RNA-seq data.

Description

Plot gene expression patterns

Usage

plotMarkers(object, genes, use.scaled = T, do.log2 = FALSE, do.order = T,
  show.jitter = T, plots = c("cell", "boxplot", "pca", "tsne"),
  dims.use = 1:2, pt.size = 1, font.size = 8, ...)

Arguments

object	A sincera object
genes	The expression patterns of genes to be plotted
use.scaled	If TRUE, use the scaled expression values for plotting
do.log2	If TRUE, apply log2 transformation to the values
do.order	If TRUE, order cells based on their GROUP information
show.jitter	If TRUE, in the violin and boxplot, plot individual cells
plots	The type of plots to be shown, possible values include cell, violin, boxplot, pca, and tsne
dims.use	A numeric vector containing the indices of the two dimensions for pca or tsne plot
pt.size	The size of points in the plot
fontsize	The size of font in the plot

minzheguo/SINCERA documentation built on Feb. 3, 2021, 2:31 p.m.