checkColormapCompatibility {iSEE} | R Documentation

## 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 incompability 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)

[Package iSEE version 1.6.1 Index]