checkColormapCompatibility: Check compatibility between ExperimentColorMap and...
In iSEE: Interactive SummarizedExperiment Explorer

Description Usage Arguments Value Author(s) Examples

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.

1	checkColormapCompatibility(ecm, se)

`ecm`	An ExperimentColorMap.
`se`	A SingleCellExperiment.

A character vector of incompability error messages, if any.

Kevin Rue-Albrecht

# 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)