plot_hexbin_meta_plus {schex} | R Documentation

## Plot of meta data with annotation of single cell data in bivariate hexagon cells.

### Description

Plot of meta data with annotation of single cell data in bivariate hexagon cells.

### Usage

    plot_hexbin_meta_plus(
      sce,
      col1,
      col2,
      action,
      no = 1,
      colors = NULL,
      title = NULL,
      xlab = NULL,
      ylab = NULL,
      expand_hull = 3,
      na.rm = FALSE,
      ...
    )

### Arguments

`sce` | A `SingleCellExperiment` or `Seurat-class` object.
`col1` | A string referring to the name of one column in the meta data of sce by which to make the outlines. Note that this should be a factor or a character.
`col2` | A string referring to the name of one column in the meta data of sce specifying what to color hexagons by.
`action` | A string specifying how meta data as specified in col2 of observations in binned hexagon cells are to be summarized. Possible actions are `prop`, `mode`, `mean` and `median` (see details).
`no` | An integer specifying which level to plot of the column. Only in effect when `action=prop`.
`colors` | A vector of strings specifying which colors to use for plotting the different levels in the selected column of the meta data.
`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.
`expand_hull` | A numeric value determining the expansion of the line marking different clusters.
`na.rm` | Logical indicating whether NA values should be removed.
`...` | Additional arguments passed on to `ggforce{geom_mark_hull}`.

### Details

This function plots any meta data in the hexagon cell representation calculated with `make_hexbin` as well as at the same time representing outlines of clusters. The chosen gene expression is summarized by one of four actions `prop_0`, `mode`, `mean` and `median`:

`prop`

  Returns the proportion of each level or unique character in the bin. The associated meta data column needs to be a factor or character.

`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.

### Value

A `ggplot2{ggplot}` object.

### Examples

    #' # For Seurat object
    library(Seurat)
    data("pbmc_small")
    pbmc_small <- make_hexbin(pbmc_small, 10, dimension_reduction = "PCA")
    pbmc_small$RNA_snn_res.0.8 <- as.factor(pbmc_small$RNA_snn_res.0.8)
    plot_hexbin_meta_plus(pbmc_small, col1="RNA_snn_res.0.8",
      col2="nCount_RNA", action="mean")
    plot_hexbin_meta_plus(pbmc_small, col1="RNA_snn_res.0.8",
      col2="groups", action="prop", no=1)

[Package schex version 1.8.0 Index]