V(D)J gene usage stacked barplots

Source: R/VDJ_Vgene_usage_stacked_barplot.R

Produces a stacked barplot with the fraction of the most frequently used IgH and IgK/L Vgenes. This function can be used in combination with the VDJ_Vgene_usage_barplot to vizualize V gene usage per sample and among samples.

VDJ_Vgene_usage_stacked_barplot(
  VDJ,
  group.by,
  HC.gene.number,
  Fraction.HC,
  LC.Vgene,
  LC.gene.number,
  Fraction.LC,
  platypus.version,
  is.bulk
)

Arguments

VDJ

Either (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, OR (for platypus version "v3") the the VDJ matrix output of the VDJ_GEX_matrix() function (normally VDJ.GEX.matrix.output[[1]])

group.by

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

HC.gene.number

Numeric value indicating the top genes to be dispayed. If this number is higher than the total number of unique HC V genes in the VDJ repertoire, then this number is equal to the number of unique HC V genes.

Fraction.HC

Numeric value indicating the minimum fraction of clones expressing a particular HC V gene. If the usage of a particular gene is below this value, then this gene is excluded. If the usage of a particular gene is above this value even in one sample, then this gene is included in the analysis. Default value is set to 0, thus all genes are selected.

LC.Vgene

Logical indicating whether to make a barplot of the LC V gene distribution. Default is set to FALSE.

LC.gene.number

Numeric value indicating the top genes to be dispayed. If this number is higher than the total number of unique LC V genes in the VDJ repertoire, then this number is equal to the number of unique LC V genes.

Fraction.LC

Numeric value indicating the minimum fraction of clones expressing a particular LC V gene. If the usage of a particular gene is below this value, then this gene is excluded. If the usage of a particular gene is above this value even in one sample, then this gene is included in the analysis. Default value is set to 0, thus all genes are selected.

platypus.version

Set according to input format to either "v2" or "v3". Defaults to "v3"

is.bulk

logical value indicating whether the VDJ input was generated from bulk-sequencing data using the bulk_to_vgm function. If is.bulk = T, the VDJ_Vgene_usage_stacked_barplot function is compatible for use with bulk data. Defaults to False (F).

Value

Returns a list of ggplot objects which show the stacked distribution of IgH and IgK/L V genes for the most used V genes. Returns an empty plot if the Fraction.HC or Fraction.LC that were selected were too high, resulting in the exclusion of all the genes.

Examples

#Platypus v3
example.vdj.vgene_usage <- VDJ_Vgene_usage_stacked_barplot(
VDJ = Platypus::small_vgm[[1]], LC.Vgene = TRUE
,HC.gene.number = 15, Fraction.HC = 1, platypus.version = "v3")
#> Sample order: s1 ; s3 ; s2