checkColormapCompatibility: Check compatibility between ExperimentColorMap and...

In csoneson/iSEE: Interactive SummarizedExperiment Explorer

Check compatibility between ExperimentColorMap and SummarizedExperiment objects

Description

This function compares a pair of ExperimentColorMap and SingleCellExperiment objects, and examines whether all of the assays, colData, and rowData defined in the ExperimentColorMap object exist in the SingleCellExperiment object.

Usage

checkColormapCompatibility(ecm, se)

Arguments

ecm	An ExperimentColorMap.
se	A SingleCellExperiment.

Value

A character vector of incompatibility error messages, if any.

Author(s)

Kevin Rue-Albrecht

Examples

# Example colormaps ----

count_colors <- function(n){
  c("black","brown","red","orange","yellow")
}

qc_color_fun <- function(n){
  qc_colors <- c("forestgreen", "firebrick1")
  names(qc_colors) <- c("Y", "N")
  return(qc_colors)
}

ecm <- ExperimentColorMap(
    assays = list(
        tophat_counts = count_colors
    ),
    colData = list(
        passes_qc_checks_s = qc_color_fun
    )
)

# Example SingleCellExperiment ----

library(scRNAseq)
sce <- ReprocessedAllenData(assays="tophat_counts")

# Test for compatibility ----

checkColormapCompatibility(ecm, sce)

csoneson/iSEE documentation built on Dec. 13, 2024, 6:14 a.m.