PLOT HEATMAP FOR A LIST OF MOTIFS (out of ChromVar produced MotifMatrix)

[matteozoia4]

Dear ArchR community,

After selecting the markerMotifs I am interested in (ChromVar MotifMatrix) :

motifs <- ("Mef2C", "Mef2A", "Mef2D", "Znf148", "Tead1", "Tead3", "Klf16", "Stat6")
markerMotifs <- getFeatures(ArchR_E9.5_QCDoubfiltered, select = paste(motifs, collapse="|"), useMatrix = "MotifMatrix")
markerMotifs <- grep("z:", markerMotifs, value = TRUE)

I would like to be able to plot a Heatmap and not a cowplot of selected Motifs.

p <- plotGroups(ArchRProj = ArchR_E9.5_QCDoubfiltered, 
                groupBy = "Clusters_Combined_PeakMatrix_50_0.2_1", 
                colorBy = "MotifMatrix", 
                name = markerMotifs,
                imputeWeights = getImputeWeights(ArchR_E9.5_QCDoubfiltered)
)

p2 <- lapply(seq_along(p), function(x){
  if(x != 1){
    p[[x]] + guides(color = FALSE, fill = FALSE) + 
      theme_ArchR(baseSize = 6) +
      theme(plot.margin = unit(c(0.1, 0.1, 0.1, 0.1), "cm")) +
      theme(
        axis.text.y=element_blank(), 
        axis.ticks.y=element_blank(),
        axis.title.y=element_blank()
      ) + ylab("")
  }else{
    p[[x]] + guides(color = FALSE, fill = FALSE) + 
      theme_ArchR(baseSize = 6) +
      theme(plot.margin = unit(c(0.1, 0.1, 0.1, 0.1), "cm")) +
      theme(
        axis.ticks.y=element_blank(),
        axis.title.y=element_blank()
      ) + ylab("")
  }
})
do.call(cowplot::plot_grid, c(list(nrow = 1, rel_widths = c(2, rep(1, length(p2) - 1))),p2))

To plot the heatmap do I have to produce a summarised experiment to be used in coomplexheatmap?

Many thanks for your help,

MZ