clust.stats.plot {iCellR}

Plotting tSNE, PCA, UMAP, Diffmap and other dim reductions

Description

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

Usage

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

Arguments

x

An object of class iCellR.

plot.type

Choose from "bar.cc", "pie.cc" , box.umi", "box.mito", "box.gene", default = "box.mito".

conds.to.plot

Choose the conditions you want to see in the plot, default = NULL (all conditions).

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"

notch

Notch the box plots, default = FALSE.

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.