iCellR (version 1.6.1)

stats.plot: Plot nGenes, UMIs and percent mito

Description

This function takes an object of class iCellR and creates QC plot.

Usage

stats.plot(
  x = NULL,
  plot.type = "three.in.one",
  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 iCellR.

plot.type

Choose from "box.umi", "box.mito", "box.gene", "box.s.phase", "box.g2m.phase","all.in.one","three.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, default = 1.

cell.transparency

Color transparency for points in "scatterplot" and "boxplot", default = 0.5.

box.color

A color for the boxes in the "boxplot", default = "red".

box.line.col

A color for the lines around the "boxplot", default = "green".

back.col

Background color, default = "white"

interactive

If set to TRUE an interactive HTML file will be created, default = TRUE.

out.name

If "interactive" is set to TRUE, the out put name for HTML, default = "plot".

Value

An object of class iCellR.

Examples

# NOT RUN {
stats.plot(demo.obj,
          plot.type = "three.in.one",
          out.name = "UMI-plot",
          interactive = FALSE,
          cell.color = "slategray3",
          cell.size = 1,
          cell.transparency = 0.5,
          box.color = "red",
          box.line.col = "green")
# }