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 = CATALYST::isotope_list)

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

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

### 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 crowellh@student.ethz.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 1.4.2 Index]