iCellR (version 1.6.1)

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"
)

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".

Value

An object of class iCellR.

Examples

# NOT RUN {
cluster.plot(demo.obj,plot.type = "umap",interactive = FALSE)

cluster.plot(demo.obj,plot.type = "tsne",interactive = FALSE)

cluster.plot(demo.obj,plot.type = "pca",interactive = FALSE)

cluster.plot(demo.obj,plot.type = "pca",col.by = "conditions",interactive = FALSE)

cluster.plot(demo.obj,plot.type = "umap",col.by = "conditions",interactive = FALSE)

cluster.plot(demo.obj,plot.type = "tsne",col.by = "conditions",interactive = FALSE)
# }