iCellR (version 1.5.1)

clono.plot: Make 2D and 3D scatter plots for clonotypes.

Description

This function takes an object of class iCellR and provides plots for clonotypes.

Usage

clono.plot(
  x = NULL,
  plot.data.type = "tsne",
  clono = 1,
  clust.dim = 2,
  cell.size = 1,
  cell.colors = c("red", "gray"),
  box.cell.col = "black",
  back.col = "white",
  cell.transparency = 0.5,
  interactive = TRUE,
  out.name = "plot"
)

Arguments

x

An object of class iCellR.

plot.data.type

Choose from "tsne" and "pca", default = "tsne".

clono

A clonotype name to be plotted, default = 1.

clust.dim

2 for 2D plots and 3 for 3D plots, default = 2.

cell.size

A number for the size of the points in the plot, default = 1.

cell.colors

Colors for heat mapping the points in "scatterplot", default = c("gray","red").

box.cell.col

Choose a color for box default = "black".

back.col

A color for the plot background, default = "black".

cell.transparency

Color transparency for points, default = 0.5.

interactive

If set to TRUE an intractive 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.