plot_hexbin_feature {schex} | R Documentation

## Plot of feature expression of single cells in bivariate hexagon cells.

### Description

Plot of feature expression of single cells in bivariate hexagon cells.

### Usage

    plot_hexbin_feature(
      sce,
      mod = "RNA",
      type,
      feature,
      action,
      title = NULL,
      xlab = NULL,
      ylab = NULL,
      lower_cutoff = 0,
      upper_cutoff = 1
    )

### Arguments

`sce` | A `SingleCellExperiment` or `Seurat-class` object.
`mod` | A string referring to the name of the modality used for plotting. For RNA modality use "RNA". For other modalities use name of alternative object for the `SingleCellExperiment` or the name of the assay for the `Seurat-class` object.
`type` | A string referring to the type of assay in the `SingleCellExperiment` object or the data transformation in the `Seurat-class` object.
`feature` | A string referring to the name of one feature.
`action` | A strings pecifying how meta data of observations in binned hexagon cells are to be summarized. Possible actions are `prop_0`, `mode`, `mean` and `median` (see details).
`title` | A string containing the title of the plot.
`xlab` | A string containing the title of the x axis.
`ylab` | A string containing the title of the y axis.
`lower_cutoff` | For `mode`, `mean` and `median` actions, remove expression values below this quantile. Expressed as decimal. Default: 0
`upper_cutoff` | For `mode`, `mean` and `median` actions, remove expression values above this quantile. Expressed as decimal. Default: 1

### Details

This function plots the expression of any feature in the hexagon cell representation calculated with `make_hexbin`. The chosen gene expression is summarized by one of four actions `prop_0`, `mode`, `mean` and `median`:

`prop_0`

  Returns the proportion of observations in the bin greater than 0. The associated meta data column needs to be numeric.

`mode`

  Returns the mode of the observations in the bin. The associated meta data column needs to be numeric.

`mean`

  Returns the mean of the observations in the bin. The associated meta data column needs to be numeric.

`median`

  Returns the median of the observations in the bin. The associated meta data column needs to be numeric.

To access the data that has been integrated in the `Seurat-class` object specifiy `mod="integrated"`.

### Value

A `ggplot2{ggplot}` object.

### Examples

    # For Seurat object
    library(Seurat)
    data("pbmc_small")
    pbmc_small <- make_hexbin(pbmc_small, 10, dimension_reduction = "PCA")
    plot_hexbin_feature(pbmc_small, type="counts", feature="TALDO1",
       action="median")
    plot_hexbin_feature(pbmc_small, type="counts", feature="TALDO1",
       action="median", lower_cutoff=0.2, upper_cutoff=0.5)
    # For SingleCellExperiment object
    ## Not run:
    library(TENxPBMCData)
    library(scater)
    tenx_pbmc3k <- TENxPBMCData(dataset = "pbmc3k")
    rm_ind <- calcAverage(tenx_pbmc3k)<0.1
    tenx_pbmc3k <- tenx_pbmc3k[!rm_ind,]
    colData(tenx_pbmc3k) <- cbind(colData(tenx_pbmc3k),
       perCellQCMetrics(tenx_pbmc3k))
    tenx_pbmc3k <- logNormCounts(tenx_pbmc3k)
    tenx_pbmc3k <- runPCA(tenx_pbmc3k)
    tenx_pbmc3k <- make_hexbin( tenx_pbmc3k, 20, dimension_reduction = "PCA")
    plot_hexbin_feature(tenx_pbmc3k, type="logcounts",
       feature="ENSG00000135250", action="median")
    plot_hexbin_feature(tenx_pbmc3k, type="logcounts",
       feature="ENSG00000135250", action="mode")

    ## End(Not run)
    # For other modalities in Seurat object
    library(Seurat)
    data("pbmc_small")
    pbmc_small <- make_hexbin(pbmc_small, 10, dimension_reduction = "PCA")
    protein <- matrix(rnorm(10* ncol(pbmc_small)), ncol=ncol(pbmc_small))
    rownames(protein) <- paste0("A", seq(1,10,1))
    colnames(protein) <- colnames(pbmc_small)
    pbmc_small[["ADT"]] <- CreateAssayObject(counts = protein)
    pbmc_small <- make_hexbin(pbmc_small, 10, dimension_reduction = "PCA")
    plot_hexbin_feature(pbmc_small, type="counts", mod="ADT",
        feature="A1", action="prop_0")

[Package schex version 1.6.3 Index]