In ccb-hms/expressionviewer: Creates a Shiny App to Display Expression of SummarizedExperiments and SGFeatureCounts

Data preparation

Prepare a SummarizedExperiment, SGFeatureCounts object, or a list composed of these object classes.

#Download data
library(celldex)
bluePrintEncode <- celldex::BlueprintEncodeData()
dice <- celldex::DatabaseImmuneCellExpressionData()
hPCA <- celldex::HumanPrimaryCellAtlasData()
mID <- celldex::MonacoImmuneData()

#Make a list of the SummarizedExperiments to display
counts <- list(bluePrintEncode, dice, hPCA, mID)

#Name the list of experiments as they are called in the local environment
names(counts) <- c("bluePrintEncode", "dice", "hPCA", "mID")

UI alterations

If the names of the experiments in a list are not what the app should display to the user, specify printNames in order to customize how they will appear in the selection menu.

#Create a list of names to describe each experiment in the app
printNames <- c("Blueprint/ENCODE",
                "Database Immune Cell Expression (DICE)",
                "Human Primary Cell Atlas (HPCA)",
                "Monaco Immune Data (MID)")

App creation

To call the app, the experiment and metaNames need to be specified - all other parameters are optional.

#Call function to create shiny app
ExpressionViewer(experiment= counts, metaNames = "label.main",
                 printNames = printNames)

ccb-hms/expressionviewer documentation built on Dec. 19, 2021, 1:58 p.m.