scater_gui: scater GUI function

In dynverse/scaterlegacy: Single-cell analysis toolkit for gene expression data in R

Description

scater shiny app GUI for workflow for less programmatically inclined users or those who would like a quick and easy way to view multiple plots.

Usage

scater_gui(sce_set)

Arguments

sce_set

SCESet object after running calculateQCMetrics on it

Value

Opens a browser window with an interactive shiny app and visualize all possible plots included in the scater

Author(s)

Davis McCarthy and Vladimir Kiselev

Examples

data("sc_example_counts")
data("sc_example_cell_info")
pd <- new("AnnotatedDataFrame", data=sc_example_cell_info)
rownames(pd) <- pd$Cell
example_sceset <- newSCESet(countData=sc_example_counts, phenoData=pd)
drop_genes <- apply(exprs(example_sceset), 1, function(x) {var(x) == 0})
example_sceset <- example_sceset[!drop_genes, ]
example_sceset <- calculateQCMetrics(example_sceset, feature_controls = 1:40)
## Not run: 
scater_gui(example_sceset)

## End(Not run)

dynverse/scaterlegacy documentation built on Feb. 17, 2020, 5:07 a.m.