cluster.plot: 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"
)

Value

An object of class iCellR.

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".