clono.plot: Make 2D and 3D scatter plots for clonotypes.
In iCellR: Analyzing High-Throughput Single Cell Sequencing Data

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

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"
)

`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".