plot_hexbin_feature_shiny: Plot of feature expression of single cell data in bivariate...

In schex: Hexbin plots for single cell omics data

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)

schex documentation built on Nov. 8, 2020, 5:56 p.m.