Get paired v gene heavy chain and light chain matrix on clonotype level. A v gene usage pheatmap can be obtain by p<-pheatmap::pheatmap(vgu_matrix,show_colnames= T, main = "V Gene Usage"), where the vgu_matrix is the output of this function.

Get paired v gene heavy chain and light chain matrix on clonotype level. A v gene usage pheatmap can be obtain by p<-pheatmap::pheatmap(vgu_matrix,show_colnames= T, main = "V Gene Usage"), where the vgu_matrix is the output of this function.

get.vgu.matrix(all.contig.annotations, level)

Arguments

all.contig.annotations

The dataframe "all_contig_annotation" from simulation output.

level

Can be "clone" or "cell". If "clone", the function will return paired v gene usage matrix on clonotype level. Otherwise it will return on cell level.

Value

a paired v gene heavy chain and light chain matrix on clonotype level.