plot_hexbin_feature_shiny {schex} | R Documentation

## Plot of feature expression of single cell data in bivariate hexagon cells as shiny instance.

### Description

Plot of feature expression of single cell data in bivariate hexagon cells as shiny instance.

### Usage

    plot_hexbin_feature_shiny(
      sce,
      mod = "RNA",
      type,
      feature,
      action,
      min_nbins,
      max_nbins,
      dimension_reduction
    )

### 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 `plot_hexbin_feature`).
`min_nbins` | The miniumum number of bins partitioning the range of the first component of the chosen dimension reduction.
`max_nbins` | The miniumum number of bins partitioning the range of the first component of the chosen dimension reduction.
`dimension_reduction` | A string indicating the reduced dimension result to calculate hexagon cell representation of.

### Details

This function opens a shiny instance, which allows to investigate the effect of the resolution parameter. The user can change the resolution using the slider. Each hexagon is clickable, which will plot the observations in the chosen hexagons in a histograms below.

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

### Value

An object that represents the app.

### See Also

`plot_hexbin_feature`

### Examples

    # For Seurat object
    ## Not run:
    library(Seurat)
    data("pbmc_small")
    plot_hexbin_feature_shiny(pbmc_small, type="counts", feature="TALDO1",
       action="median", min_nbins=2, max_nbins=10, dimension_reduction="PCA",
       mod="RNA")

    ## End(Not run)

[Package schex version 1.6.3 Index]