cluster.plot: Plot nGenes, UMIs and perecent mito

In rezakj/scSeqR: scSeqR; a toolkit to analyze single cell sequencing data types (i.e scRNA-seq) and large numeric matrix files.

Plot nGenes, UMIs and perecent mito

Description

This function takes an object of class scSeqR and creats plot.

Usage

cluster.plot(x = NULL, cell.size = 1, plot.type = "tsne",
  cell.color = "black", back.col = "white", col.by = "clusters",
  cond.shape = F, cell.transparency = 0.5, clust.dim = 2,
  angle = 20, density = F, interactive = TRUE, static3D = F,
  out.name = "plot")

Arguments

x	An object of class scSeqR.
cell.size	A numeric value for the size of the cells, defults = 1.
plot.type	Choose between "tsne" and "pca", defult = "tsne".
cell.color	Choose cell color if col.by = "monochrome", defult = "black".
back.col	Choose background color, defult = "black".
col.by	Choose between "clusters", "conditions" or "monochrome", defult = "clusters".
cell.transparency	A numeric value between 0 to 1, defult = 0.5.
clust.dim	A numeric value for plot dimentions. Choose either 2 or 3, defult = 2.
angle	A number to rotate the non-interactive 3D plot.
density	If TRUE the density plots for PCA/tSNE second dimention will be created, defult = FALSE.
interactive	If TRUE an html intractive file will be made, defult = TRUE.
out.name	Output name for html file if interactive = TRUE defult = "plot".

Value

An object of class scSeqR.

Examples

## Not run: 
tsne.plot(my.obj)

## End(Not run)

rezakj/scSeqR documentation built on March 28, 2022, 12:17 p.m.