Hello
I am trying get heat map with Vsn-pyScenic pipeline generated output by Average regular activity by cluster code
The complex heat map generated regulons are many per cell type. How can I control the number of top regulons shown in the map from the code?
The next chunk of code for %regulon activity is not working with the pipeline generated output. I tried to read the binaryRegulonActivity with regulonsAucThresholds, but it doesn't work.
minPerc <- .7
binaryRegulonActivity <- regulonsAucThresholds
cellInfo_binarizedCells <- cellInfo[which(rownames(cellInfo)%in% colnames(binaryRegulonActivity)),, drop=FALSE]
regulonActivity_byCellType_Binarized <- sapply(split(rownames(cellInfo_binarizedCells), cellInfo_binarizedCells$CellType),
function(cells) rowMeans(binaryRegulonActivity[,cells, drop=FALSE]))
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'rowMeans': incorrect number of dimensions
This code worked with no issues with R genie output with downsampled data.
Is there anything I can change to get this code working for pipeline generated output?
Thanks
GreyRock
Hello I am trying get heat map with Vsn-pyScenic pipeline generated output by Average regular activity by cluster code The complex heat map generated regulons are many per cell type. How can I control the number of top regulons shown in the map from the code? The next chunk of code for %regulon activity is not working with the pipeline generated output. I tried to read the binaryRegulonActivity with regulonsAucThresholds, but it doesn't work. minPerc <- .7 binaryRegulonActivity <- regulonsAucThresholds cellInfo_binarizedCells <- cellInfo[which(rownames(cellInfo)%in% colnames(binaryRegulonActivity)),, drop=FALSE] regulonActivity_byCellType_Binarized <- sapply(split(rownames(cellInfo_binarizedCells), cellInfo_binarizedCells$CellType), function(cells) rowMeans(binaryRegulonActivity[,cells, drop=FALSE]))
Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'rowMeans': incorrect number of dimensions
This code worked with no issues with R genie output with downsampled data. Is there anything I can change to get this code working for pipeline generated output? Thanks GreyRock