Get information about the clonotype counts grouped by transcriptome state(cell type).

Plot a stacked barplot for clonotype counts grouped by transcriptome state(cell type).

clonofreq.trans.plot(
  all.contig.annotations,
  history,
  trans.names,
  top.n,
  y.limit,
  colors
)

Arguments

all.contig.annotations: The output dataframe all_contig_annotation from function simulate.repertoire.
history: The dataframe history from simulate output.
trans.names: The names of cell types which are used in transcriptome.switch.prob argument in the simulation.
top.n: The top n abundant clones to be shown in the plot. If missing, all clones will be shown.
y.limit: The upper limit for y axis in the plot.
colors: A named character vector of colors, the names are the isotypes. If missing, the default has 11 colors coresponding to the default isotype names.

a stacked barplot for clonotype counts grouped by transcriptome state(cell type).