Visualise flux matrix describing class-switch recombination (CSR) transitions in data

plotFluxMatrix parse data from fitTPT() and visualises the estimated isotype-switching dynamics in the form of a flux matrix detailing amount of switches from and to each isotype.

Usage

plotFluxMatrix(
  TPTObj,
  SeuratObj,
  ighc_count_assay_name = "IGHC",
  mask_improbable_csr = TRUE,
  return_plot = TRUE
)

Arguments

TPTObj

List of TPT results, output from the fitTPT function.

SeuratObj

Seurat object

ighc_count_assay_name

name of assay in SeuratObj which holds the IgH productive/sterile transcript counts. (Default: "IGHC")

mask_improbable_csr

Should isotype combinations which represents improbable Class-switch recombination events (i.e. switching back to an isotype 5' to the current one) be removed from visualisation? (Default: TRUE)

return_plot

Should the CSR transition plot be returned? If FALSE, a named list of stationary_distribution and flux will be returned which contains the data frames to be visualised in this plot. (Default: TRUE)

Value

A ggplot2 object showing the flux matrix and the associated significance level in the form a bubble plot. See 'Description' for details.

Details

plotFluxMatrix parses data from the fitTPT() function and visualises the results from Transition Path Theory (TPT) in the form of a bubble plot representing the amount of flux from and to each isotype. * The bubble size is scaled by significance, i.e. the likelihood that the observed flux is greater than randomised flux estimates obtained by reshuffling columns of the transition matrix. * The bubble colour is scaled by magnitude, i.e. the amount of flux estimated to flow from one isotype to another isotype. * Improbable CSR combinations (i.e. switching back to an isotype preceding the current isotype) are removed by default. This can be turned off by indicating mask_improbable_csr = FALSE.