Plot isoform PI or expression along pseudotime with annotation bands

Visualizes isoform-level usage or expression for a given gene along pseudotime, together with one or multiple categorical annotations displayed as horizontal bands (e.g. cell type, cell cycle phase). The two most abundant isoforms of the gene are shown.

Usage

IsoformPseudotimePlot(
  seurat_obj,
  gene,
  pseudotime_col,
  band_cols = "cell_type",
  assay = "ISO",
  slot = "counts",
  mode = c("PI", "exp"),
  delimiter = "\\.\\.",
  nbins = 100
)

Arguments

seurat_obj

A Seurat object.

gene

Character scalar. Gene name used as prefix for isoform IDs (e.g. "GeneA" for rows like "GeneA..Tx1").

pseudotime_col

Name of the metadata column containing pseudotime values.

band_cols

Character vector of metadata column names to display as annotation bands (e.g. c("cell_type", "Phase")). Each should be a categorical variable.

assay

Assay name containing isoform-level counts. Default: "ISO".

slot

Slot of the assay to use (e.g. "counts", "data"). Default: "counts".

mode

Either "PI" (default) to plot isoform Percent Inclusion (per-cell proportions across isoforms of the gene) or "exp" to plot raw isoform expression.

delimiter

Regex delimiter between gene and isoform ID. Default: "\\.\\.".

nbins

Integer. Number of bins along pseudotime for aggregating annotation bands. Default: 100.

Value

A patchwork object combining the annotation band plot(s) and the isoform trend plot.

Examples

if (FALSE) { # \dontrun{
library(Seurat)
library(Matrix)

set.seed(123)

iso_names <- c("GeneA..Tx1", "GeneA..Tx2", "GeneA..Tx3")
mat <- Matrix(
  rpois(300, lambda = 10),
  nrow = 3,
  sparse = TRUE,
  dimnames = list(iso_names, paste0("Cell", 1:100))
)

obj <- CreateSeuratObject(counts = mat, assay = "ISO")
obj$pseudotime <- sort(runif(100, 0, 1))
obj$cell_type  <- sample(c("Tumor", "Stromal", "Immune"), 100, TRUE)
obj$Phase      <- sample(c("G1", "S", "G2M"), 100, TRUE)

IsoformPseudotimePlot(
  seurat_obj     = obj,
  gene           = "GeneA",
  pseudotime_col = "pseudotime",
  band_cols      = c("cell_type", "Phase"),
  assay          = "ISO",
  mode           = "PI"
)
} # }