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",
  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"
)

Value

An object of class iCellR.

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".