cluster.plot: Plot nGenes, UMIs and perecent mito
In rezakj/iCellR: Analyzing High-Throughput Single Cell Sequencing Data

cluster.plot

R Documentation

Plot nGenes, UMIs and perecent mito

Description

This function takes an object of class iCellR and creates plots to see the clusters.

Usage

cluster.plot(
  x = NULL,
  cell.size = 0.5,
  plot.type = "tsne",
  cell.color = "black",
  back.col = "white",
  col.by = "clusters",
  cond.facet = FALSE,
  cond.shape = FALSE,
  anno.clust = FALSE,
  anno.size = 4,
  cell.transparency = 1,
  clust.dim = 2,
  angle = 20,
  clonotype.max = 10,
  density = FALSE,
  interactive = TRUE,
  static3D = FALSE,
  out.name = "plot"
)

Arguments

`x`	An object of class iCellR.
`cell.size`	A numeric value for the size of the cells, default = 1.
`plot.type`	Choose between "tsne", "pca", "umap", "knetl", "diffusion", default = "tsne".
`cell.color`	Choose cell color if col.by = "monochrome", default = "black".
`back.col`	Choose background color, default = "black".
`col.by`	Choose between "clusters", "conditions", "cc" (cell cycle) or "monochrome", default = "clusters".
`cond.facet`	Show the conditions in separate plots.
`cond.shape`	If TRUE the conditions will be shown in shapes.
`anno.clust`	Annotate cluster names on the plot, default = TRUE.
`anno.size`	If anno.clust is TRUE set font size, default = 3.
`cell.transparency`	A numeric value between 0 to 1, default = 0.5.
`clust.dim`	A numeric value for plot dimensions. Choose either 2 or 3, default = 2.
`angle`	A number to rotate the non-interactive 3D plot.
`clonotype.max`	Number of clonotype to plot, default = 10.
`density`	If TRUE the density plots for PCA/tSNE second dimension will be created, default = FALSE.
`interactive`	If TRUE an html interactive file will be made, default = TRUE.
`static3D`	If TRUE a non-interactive 3D plot will be made.
`out.name`	Output name for html file if interactive = TRUE, default = "plot".