clono.plot {iCellR}

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",
  clonotype.column = 1,
  barcode.column = 2,
  clono = NULL,
  conds.to.plot = NULL,
  clust.dim = 2,
  cell.size = 1,
  cell.colors = c("red", "gray"),
  box.cell.col = "black",
  back.col = "white",
  cell.transparency = 1,
  interactive = TRUE,
  out.name = "plot"
)

Arguments

x

An object of class iCellR.

plot.data.type

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

clonotype.column

The column which has the clonotype IDs, default = 2.

barcode.column

The column which has the barcode IDs, default = 1.

clono

A clonotype name to be plotted, default = NULL.

conds.to.plot

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

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.