stats.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 QC plot.

Usage

stats.plot(x = NULL, plot.type = "box.umi",
  cell.color = "slategray3", cell.size = 1, cell.transparency = 0.5,
  box.color = "red", box.line.col = "green", back.col = "white",
  interactive = TRUE, out.name = "plot")

Arguments

x	An object of class scSeqR.
plot.type	Choose from "box.umi", "box.mito", "box.gene", "box.s.phase", "box.g2m.phase","all.in.one", "point.mito.umi", "point.gene.umi".
cell.color	Choose a color for points in the plot.
cell.size	A number for the size of the points in the plot, defult = 1.
cell.transparency	Color transparency for points in "scatterplot" and "boxplot", defult = 0.5.
box.color	A color for the boxes in the "boxplot", defult = "red".
box.line.col	A color for the lines around the "boxplot", defult = "green".
interactive	If set to TRUE an intractive HTML file will be created, defult = TRUE.
out.name	If "interactive" is set to TRUE, the out put name for HTML, defult = "plot".

Value

An object of class scSeqR.

Examples

## Not run: 
stats.plot(my.obj,
          plot.type = "box.gene.umi.mito",
          out.name = "UMI-plot",
          interactive = F,
          cell.color = "slategray3",
          cell.size = 1,
          cell.transparency = 0.5,
          box.color = "red",
          box.line.col = "green",
          back.col = "white")

stats.plot(my.obj, plot.type = "point.gene.umi", interactive = T, out.name = "scatter.gene.umi")

stats.plot(my.obj, plot.type = "point.mito.umi", interactive = T, out.name = "scatter.mito.umi")

## End(Not run)

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