AUCell_createViewerApp: Create AUCell viewer app

In AUCell: AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

Description

Creates a Shiny app to explore AUCell results

Usage

AUCell_createViewerApp(
  auc,
  thresholds = NULL,
  tSNE = NULL,
  exprMat = NULL,
  cellInfo = NULL,
  colVars = NULL
)

Arguments

auc	AUC object returned by AUCell_calcAUC
thresholds	Thresholds corresponding to each gene set (optional)
tSNE	t-SNE coordinates for the cells (optional). The row names should correspond to the cell ID. The column names should be "tsne1" and "tsne2".
exprMat	Expression matrix (optional)
cellInfo	Phenodata (optional)
colVars	Color for the phenodata variables (as list, optional)

Value

Thresholds and cells selected within the app (as list).

Note

With lasso: "To make a multiple selection, press the SHIFT key. To clear the selection, press the ESC key."

Examples

######
# Fake run of AUCell
set.seed(123)
exprMatrix <- matrix(
  data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
  nrow=20, 
  dimnames=list(paste("Gene", 1:20, sep=""), 
                paste("Cell", 1:500, sep="")))
geneSets <- list(geneSet1=sample(rownames(exprMatrix), 10),
                 geneSet2=sample(rownames(exprMatrix), 5))

cells_rankings <- AUCell_buildRankings(exprMatrix)
cells_AUC <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5, nCores=1)
selectedThresholds <- NULL
# cellsTsne<- Rtsne::Rtsne(t(exprMatrix),max_iter = 10)$Y
cellsTsne<- tsne::tsne(t(exprMatrix),max_iter = 10)
rownames(cellsTsne) <- colnames(exprMatrix)

cellInfo <- data.frame(cellType1=sample(LETTERS[1:3],ncol(exprMatrix), replace=TRUE), 
                       cellType2=sample(letters[5:7],ncol(exprMatrix), replace=TRUE), 
                       nGenes=abs(rnorm(ncol(exprMatrix))), 
                       row.names=colnames(exprMatrix))
######

# Create app 
aucellApp <- AUCell_createViewerApp(auc=cells_AUC, thresholds=selectedThresholds, 
                                    tSNE=cellsTsne, exprMat=exprMatrix, cellInfo=cellInfo)

# The exact commands to lauch the app depend on the R settings 
# For example:
# library(shiny)
# options(shiny.host="0.0.0.0") 
# savedSelections <- runApp(aucellApp) 
# (see Shiny's doc for help)

AUCell documentation built on Nov. 8, 2020, 5:51 p.m.