plotSpillmat {CATALYST}R Documentation

Spillover matrix heat map

Description

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

Usage

plotSpillmat(bc_ms, SM, ...)

## S4 method for signature 'numeric,matrix'
plotSpillmat(bc_ms, SM, out_path = NULL,
  name_ext = NULL, annotate = TRUE, plotly = TRUE,
  isotope_list = NULL)

## S4 method for signature 'ANY,data.frame'
plotSpillmat(bc_ms, SM, out_path = NULL,
  name_ext = NULL, annotate = TRUE, plotly = TRUE,
  isotope_list = NULL)

## S4 method for signature 'character,ANY'
plotSpillmat(bc_ms, SM, out_path = NULL,
  name_ext = NULL, annotate = TRUE, plotly = TRUE,
  isotope_list = NULL)

Arguments

bc_ms

a vector of numeric masses corresponding to barcode channels.

SM

spillover matrix returned from computeSpillmat.

...

optional arguments.

out_path

character string. If specified, outputs will be generated here.

name_ext

character string. If specified, will be appended to the plot's name.

annotate

logical. If TRUE (default), spill percentages are shown inside bins and rows are annotated with the total amount of spill received.

plotly

logical. Should an interactive plot be rendered?

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.

Value

Plots estimated spill percentages as a heat map. Colours are ramped to the highest spillover value present

Author(s)

Helena Lucia Crowell helena.crowell@uzh.ch

Examples

# get single-stained control samples
data(ss_exp)

# specify mass channels stained for
bc_ms <- c(139, 141:156, 158:176)

re <- assignPrelim(x = ss_exp, y = bc_ms)
re <- estCutoffs(x = re)
re <- applyCutoffs(x = re)
spillMat <- computeSpillmat(x = re)
plotSpillmat(bc_ms = bc_ms, SM = spillMat)


[Package CATALYST version 1.8.2 Index]