V(D)J gene usage stacked barplots

Source: R/VDJ_Vgene_usage.R

Produces a matrix counting the number of occurences for each VDJ and VJ Vgene combinations for each list enty in VDJ.clonotype.output or for each sample_id in VDJ.matrix

VDJ_Vgene_usage(VDJ, group.by, platypus.version)

Arguments

VDJ

For platypus.version = "v2" output from VDJ_analyze function. This should be a list of clonotype dataframes, with each list element corresponding to a single VDJ repertoire. For platypus.version = "v3" output VDJ dataframe from VDJ_GEX_matrix function (VDJ_GEX_matrix.output[[1]])

group.by

Character. Defaults to "sample_id". Column name of VDJ to group plot by.

platypus.version

Character. Defaults to "v3". Can be "v2" or "v3" dependent on the input format

Value

Returns a list of matrices containing the number of Vgene heavy/light chain combinations per repertoire.

Examples

example.vdj.vgene_usage <- VDJ_Vgene_usage(VDJ =
Platypus::small_vgm[[1]], platypus.version = "v3")