AnnotationScatterPlot {ILoReg} | R Documentation

## Visualiation of a custom annotation over nonlinear dimensionality reduction

### Description

The AnnotationScatterPlot enables visualizing arbitrary class labels over the nonliner dimensionality reduction, e.g. t-SNE or UMAP.

### Usage

    AnnotationScatterPlot.SingleCellExperiment(
      object,
      annotation,
      return.plot,
      dim.reduction.type,
      point.size,
      show.legend
    )

    ## S4 method for signature 'SingleCellExperiment'
    AnnotationScatterPlot(
      object,
      annotation = NULL,
      return.plot = FALSE,
      dim.reduction.type = "",
      point.size = 0.7,
      show.legend = FALSE
    )

### Arguments

`object` | of `SingleCellExperiment` class
`annotation` | a character vector, factor or numeric for the class labels.
`return.plot` | return.plot whether to return the ggplot2 object or just draw it. Default is `FALSE`.
`dim.reduction.type` | "tsne" or "umap". Default is `tsne`.
`point.size` | point size. Default is `0.7`.
`show.legend` | a logical denoting whether to show the legend on the right side of the plot. Default is `TRUE`.

### Value

ggplot2 object if return.plot=TRUE

### Examples

    library(SingleCellExperiment)
    sce <- SingleCellExperiment(assays = list(logcounts = pbmc3k_500))
    sce <- PrepareILoReg(sce)
    ## These settings are just to accelerate the example, use the defaults.
    sce <- RunParallelICP(sce,L=2,threads=1,C=0.1,k=5,r=1)
    sce <- RunPCA(sce,p=5)
    sce <- RunTSNE(sce)
    sce <- HierarchicalClustering(sce)
    sce <- SelectKClusters(sce,K=5)
    ## Change the names to the first five alphabets and Visualize the annotation.
    custom_annotation <- plyr::mapvalues(metadata(sce)$iloreg$clustering.manual,
                                         c(1,2,3,4,5),
                                         LETTERS[1:5])
    AnnotationScatterPlot(sce,
                          annotation = custom_annotation,
                          return.plot = FALSE,
                          dim.reduction.type = "tsne",
                          show.legend = FALSE)

[Package ILoReg version 1.2.0 Index]