VDJ_clonal_expansion: Flexible wrapper for clonal expansion barplots by isotype,...

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Flexible wrapper for clonal expansion barplots by isotype, GEX cluster etc.

Description

Clonal frequency plot displaying clonal expansion for either T and B cells with Platypus VDJ_build() output. For Platypus v2 plotting of B cell clonotype expansion and isotypes please refer to VDJ_isotypes_per_clone.

Usage

VDJ_clonal_expansion(
  VDJ,
  celltype,
  clones,
  subtypes,
  isotypes.to.plot,
  species,
  treat.incomplete.clones,
  treat.incomplete.cells,
  group.by,
  color.by,
  variant.plot,
  text.size
)

Arguments

VDJ	VDJ dataframe generated using the VDJ_build function.
celltype	Character. Either "Tcells" or "Bcells". If set to Tcells bars will not be colored by default and the parameters treat_incomplete_cells, treat_incomplete_clones, subtypes and species are ignored. The color.by and group.by arguments work identically for both celltypes. If none provided it will detect this param from the celltype column.
clones	numeric value indicating the number of clones to be considered for the clonal expansion plot. Default value is 50. For a standard plot more than 50 is discouraged. When showing only one - possibly rare - isotype via isotypes.to.plot it may be useful to set this number higher (e.g. 100-200)
subtypes	Logical indicating whether to display isotype subtypes or not.
isotypes.to.plot	Character vector. Defaults to "all". This can be set to any number of specific Isotypes, that are to be shown exclusively. For example, to show only clones containing IgG, input "IGHG". If only wanting to check clones with IgA and IgD input c("IGHA","IGHD"). Works equally if subtypes are set to TRUE. Is ignored if color.by is not set to "isotype"
species	Character indicating whether the samples are from "Mouse" or "Human". Default is "Human".
treat.incomplete.clones	Character indicating how to proceed with clonotypes lacking a VDJC (in other words, no cell within the clonotype has a VDJC). "exclude" removes these clonotypes from the analysis. "include" keeps these clonotypes in the analysis. In the plot they will appear has having an unknown isotype.
treat.incomplete.cells	Character indicating how to proceed with cells assigned to a clonotype but missing a VDJC. "proportional" to fill in the VDJ isotype according to the proportions present in of clonotype (in case present proportions are not replicable in the total number of cells e.g. 1/3 in 10 cells, values are rounded to the next full integer and if the new counts exceed the total number of cells, 1 is subtracted from the isotype of highest frequency. If the number is below the number of cell, 1 is added to the isotype with lowest frequency to preserve diversity), "exclude" to exclude them from analysis and rank clonotypes only by the number of cells with a heavy chain. This ranking may deviate from the frequency column in the clonotype table. CAVE: if treat_incomplete_cells is set to "exclude", clonotypes lacking a VDJC entierly will be removed from the analysis. This results in a similar but not identical output as when treat_incomplete_clones is set to true. The two parameters are thereby non-redundant.
group.by	Character. Defaults to "sample_id". Column name of VDJ to split VDJ by. For each unique entry in that column a plot will be generated. Therefore plots can be generated by sample_id, group_id or any other metadata item.To get plots for the whole repertoire set to "none"
color.by	Character. Defaults to "isotype". If set to "isotype" bars are colored by the respective IgH chain or in grey for T cells. This can alternatively be set to any column name of the VDJ. This allows coloring clones by their V_gene usage or by GEX clusters
variant.plot	Logical indicating whether to plot the output showing the variants or not.
text.size	Numeric value indicating the size of the text in the plot. Default is 12.

Value

Returns a nested list. out[[1]] are plots out[[2]] are raw datatables containing also barcode and CDR3 information

Examples

clonal_out <- VDJ_clonal_expansion(VDJ = Platypus::small_vdj,
 celltype = "Bcells", clones = 30,subtypes = FALSE, species = "Mouse"
 ,treat.incomplete.clones = "exclude"
 ,treat.incomplete.cells = "proportional")
clonal_out[[1]] #list of plots
clonal_out[[2]] #list of source dataframes

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.