View source: R/VDJ_clonal_donut.R
VDJ_clonal_donut | R Documentation |
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
)
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" |
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
VDJ_clonal_donut(VDJ = Platypus::small_vgm[[1]])
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