AUCell_createViewerApp {AUCell} | R Documentation |
Creates a Shiny app to explore AUCell results
AUCell_createViewerApp( auc, thresholds = NULL, tSNE = NULL, exprMat = NULL, cellInfo = NULL, colVars = NULL )
auc |
AUC object returned by |
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) |
Thresholds and cells selected within the app (as list).
With lasso: "To make a multiple selection, press the SHIFT key. To clear the selection, press the ESC key."
###### # 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)