plotSpillmat: Spillover matrix heatmap
In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

plotSpillmat

R Documentation

Spillover matrix heatmap

Description

Generates a heatmap of the spillover matrix annotated with estimated spill percentages.

Usage

plotSpillmat(
  x,
  sm = NULL,
  anno = TRUE,
  isotope_list = CATALYST::isotope_list,
  hm_pal = c("white", "lightcoral", "red2", "darkred"),
  anno_col = "black"
)

Arguments

`x`	a `SingleCellExperiment`.
`sm`	spillover matrix to visualize. If NULL, `plotSpillmat` will try and access `metadata(x)$spillover_matrix`.
`anno`	logical. If TRUE (default), spill percentages are shown inside bins and rows are annotated with the total amount of spill received.
`isotope_list`	named list. Used to validate the input spillover matrix. Names should be metals; list elements numeric vectors of their isotopes. See `isotope_list` for the list of isotopes used by default.
`hm_pal`	character vector of colors to interpolate.
`anno_col`	character string specifying the color to use for bin annotations.

Value

a ggplot2-object showing estimated spill percentages as a heatmap with colors ramped to the highest spillover value present.

Author(s)

Helena L Crowell helena.crowell@uzh.ch

Examples

# get single-stained control samples & construct SCE
data(ss_exp)
sce <- prepData(ss_exp)

# debarcode single-positive populations
bc_ms <- c(139, 141:156, 158:176)
sce <- assignPrelim(sce, bc_ms, verbose = FALSE)
sce <- applyCutoffs(estCutoffs(sce))

# estimate & visualize spillover matrix
sce <- computeSpillmat(sce)
plotSpillmat(sce)

HelenaLC/CATALYST documentation built on Oct. 16, 2024, 12:21 a.m.