Hi everyone,

I would like to know if there is a way to plot using plotHeatmap data from two matrices generated using computeMatrix. I basically have two different BED files with a subset of genes from a whole genome, and I used that data in combination with a signal data in bigwig from ChIP-seq to generate one matrix to use plotHeatmap and obtain a metaplot representing the mean of each group of genes. I use the scale-regions version. However, I would like to combine both matrices and obtain a single plot with two lines representing the mean for each group of genes.

I have tried generating the matrices as I said, separatedly and then relabel them with computeMatrixOperations relabel and later use computeMatrixOperations rbind to merge both. However when later I use plotHeatmap --matrixFile input_matrixMerged --plotFileFormat 'png' --sortRegions 'descend' --sortUsing 'mean' --averageTypeSummaryPlot 'mean' --plotType 'lines' --missingDataColor 'black' --alpha '1.0' --xAxisLabel 'distance from START (bp)' --yAxisLabel 'signal' --heatmapWidth 7.5 --heatmapHeight 25.0 --whatToShow 'plot, heatmap and colorbar' --startLabel 'TSS' --endLabel 'STOP' --refPointLabel 'START' --legendLocation 'best' --labelRotation '0' --perGroup -o o.png Doesn't matter that I use the --perGroup argument it calculate the mean for both matrices mixed togheter.

Probably the solution must be very simple but I am unable to find a solution by now.

Thank you in advance.