Circular VDJ expansion plots — VDJ_clonal

Generate circular plots of clonal expansion per repertoire directly from the VDJ matrix of the VDJ_GEX_matrix function

VDJ_clonal_donut(
  VDJ,
  counts.to.use,
  label.size,
  not.expanded.label.vjust,
  not.expanded.label.hjust,
  total.label.vjust,
  total.label.hjust,
  expanded.colors,
  non.expanded.color
)

Arguments

VDJ: VDJ dataframe generated using the VDJ_GEX_matrix function (VDJ_GEX_matrix.output[[1]]). Plots will be made by sample and using the clonal frequencies specified by counts.to.use
counts.to.use: How to count clonotypes and cells. A column name of the VDJ matrix containing clonotype IDs. This defaults to "clonotype_id_10x", which reflects clonotypes by Cellranger in an unaltered VGM. To use counts from the VDJ_clonotype_v3 function set this parameter to the relevant column e.g. "clonotype_id_cdr.aa" or "global_clonotype_id_cdr.aa" are two examples.
label.size: Size of text labels. All parameters below are purely for graphical purposes and optional. If necessary changes should be made in small (0.1) increments. ! It is recommended to optimize these ONLY once a format for saving the plot is set.
not.expanded.label.vjust: Numeric. Regulates the vertical position of the label for non expanded cells
not.expanded.label.hjust: Numeric. Regulates the horizontal position of the label for non expanded cells
total.label.vjust: Numeric. Regulates the vertical position of the center label
total.label.hjust: Numeric. Regulates the horizontal position of the center label
expanded.colors: Character vector. Colors to use for expanded clones. Should be more than 3 for better visibility. Defaults to a "darkorchid3"-based palette.
non.expanded.color: Character. Color to use for non expanded clones. Defaults to "black"

Value

Returns a list of circular plots showing proportions of expanded clones and non-expanded clones. One plot is generated for each sample in the sample_id column

Examples

VDJ_clonal_donut(VDJ = Platypus::small_vgm[[1]])
#> Using column clonotype_id_10x for counting clones
#> Clones: Expanded: 0 / 0%; 1 cell 28 / 100%; total: 28
#> Cells: Expanded: 0 / 0%; 1 cell 28 / 100%; Total: 28
#> Clones: Expanded: 0 / 0%; 1 cell 9 / 100%; total: 9
#> Cells: Expanded: 0 / 0%; 1 cell 9 / 100%; Total: 9
#> Clones: Expanded: 0 / 0%; 1 cell 13 / 100%; total: 13
#> Cells: Expanded: 0 / 0%; 1 cell 13 / 100%; Total: 13
#> [[1]]

#> 
#> [[2]]

#> 
#> [[3]]

#>