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#' Plot UMAP results either on already run results or run first and then plot.
#'
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#' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved
#' dimension reduction components. Required
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#' @param colorBy color by a condition(any column of the annotation data).
#' @param shape add shapes to each condition.
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#' @param reducedDimName saved dimension reduction name in the
#' \linkS4class{SingleCellExperiment} object. Required.
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#' @param runUMAP If the dimension reduction components are already available
#' set this to FALSE, otherwise set to TRUE. Default is False.
#' @param useAssay Indicate which assay to use. The default is "logcounts"
#'
#' @return a UMAP plot of the reduced dimensions.
#' @export
#'
#' @examples
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#' data(scExample, package = "singleCellTK")
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#' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
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#' sce <- runQuickUMAP(sce)
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#' plotUMAP(sce)
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plotUMAP <- function(inSCE, colorBy = NULL, shape = NULL,
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reducedDimName = "UMAP", runUMAP = FALSE,
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useAssay = "counts"){
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if(!(reducedDimName %in% names(SingleCellExperiment::reducedDims(inSCE)))){
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if (runUMAP){
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inSCE <- runQuickUMAP(inSCE, useAssay = useAssay,
reducedDimName = reducedDimName)
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} else {
stop(reducedDimName,
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" dimension not found. Run `runUMAP()` or set `runUMAP` to `TRUE`.")
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}
}
UMAPDf <- data.frame(SingleCellExperiment::reducedDim(inSCE,
reducedDimName))
if (ncol(UMAPDf) > 2){
warning("More than two UMAP dimensions. Using the first two.")
}
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colnames(UMAPDf)[1] <- "UMAP1"
colnames(UMAPDf)[2] <- "UMAP2"
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xdim <- colnames(UMAPDf)[1]
ydim <- colnames(UMAPDf)[2]
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if (!is.null(colorBy)){
UMAPDf$color <- SingleCellExperiment::colData(inSCE)[, colorBy]
}
if (!is.null(shape)){
UMAPDf$shape <- factor(SingleCellExperiment::colData(inSCE)[, shape])
}
UMAPDf$Sample <- colnames(inSCE)
g <- ggplot2::ggplot(UMAPDf, ggplot2::aes_string(xdim, ydim,
label = "Sample")) +
ggplot2::geom_point()
if (!is.null(colorBy)){
g <- g + ggplot2::aes_string(color = "color") +
ggplot2::labs(color = colorBy)
}
if (!is.null(shape)){
g <- g + ggplot2::aes_string(shape = "shape") +
ggplot2::labs(shape = shape)
}
return(g)
}
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