Synchronize assay colormaps to match those in a SummarizedExperiment

This function returns an updated ExperimentColorMap in which colormaps in the assays slot are ordered to match the position of their corresponding assay in the SingleCellExperiment object. Assays in the SingleCellExperiment that do not have a match in the ExperimentColorMap are assigned the appropriate default colormap.

Usage

synchronizeAssays(ecm, se)

Arguments

ecm: An ExperimentColorMap.
se: A SingleCellExperiment.

Value

An ExperimentColorMap with colormaps in the assay slot synchronized to match the position of the corresponding assay in the SingleCellExperiment.

Details

It is highly recommended to name all assays in both ExperimentColorMap and SummarizedExperiment prior to calling this function, as this will facilitate the identification of matching assays between the two objects. In most cases, unnamed colormaps will be dropped from the new ExperimentColorMap object.

The function supports three main situations:

If all assays in the SingleCellExperiment are named, this function will populate the assays slot of the new ExperimentColorMap with the name-matched colormap from the input ExperimentColorMap, if available. Assays in the SingleCellExperiment that do not have a colormap defined in the ExperimentColorMap are assigned the appropriate default colormap.
If all assays in the SingleCellExperiment are unnamed, this function requires that the ExperimentColorMap supplies a number of assay colormaps identical to the number of assays in the SingleCellExperiment object. In that case, the ExperimentColorMap object will be returned as is.
If only a subset of assays in the SingleCellExperiment are named, this function will ignore unnamed colormaps in the ExperimentColorMap; It will populate the assays slot of the new ExperimentColorMap with the name-matched colormap from the input ExperimentColorMap, if available. Assays in the SingleCellExperiment that are unnamed, or that do not have a colormap defined in the ExperimentColorMap are assigned the appropriate default colormap.

Author

Kevin Rue-Albrecht

Examples


# Example ExperimentColorMap ----

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

ecm <- ExperimentColorMap(
    assays = list(
        counts = count_colors,
        tophat_counts = count_colors,
        cufflinks_fpkm = fpkm_colors,
        rsem_counts = count_colors,
        orphan = count_colors,
        orphan2 = count_colors,
        count_colors,
        fpkm_colors
    )
)

# Example SingleCellExperiment ----

library(scRNAseq)
sce <- ReprocessedAllenData(assays="tophat_counts")
library(scater)
sce <- logNormCounts(sce, exprs_values="tophat_counts")
sce <- runPCA(sce)
sce <- runTSNE(sce)

# Example ----

ecm_sync <- synchronizeAssays(ecm, sce)
#> Warning: Unused assays dropped from ecm: unnamed [7,8], named [counts,cufflinks_fpkm,rsem_counts,orphan,orphan2]