AUCell_createViewerApp {AUCell} | R Documentation

## Create AUCell viewer app

### 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)

[Package AUCell version 1.9.8 Index]