Heatmap based on a cluster of samples, not between clusters

[strawberry789]

How is it possible to plot a heatmap that's based on a particular cluster of different samples rather than different clusters of the integrated dataset?

[rcorces]

Sorry - I do not think I understand the question.

[strawberry789]

Sorry, I should phrase it better. Instead of a heatmap that compares between clusters of an integrated dataset, is it possible to generate a heatmap that compares a specific cluster between the different samples in the integrated dataset? - Thanks.

[rcorces]

I'm not sure if this answers your question but comparisons in ArchR are generally driven by selecting a column in cellColData. So you should think about adding a new column in cellColData that represents the comparison that you want to make.

[strawberry789]

The cellColData would be sample. Would something like the following command work:

heatmapEM <- plotEnrichHeatmap(enrichMotifs, n = 20, cutOff = 10, transpose = TRUE, colorBy = "cellColData", name = "Sample")

Instead of colorBy, what should the option name be?

[strawberry789]

I was able to generate a heatmap that consists of only the cluster of cells I wanted using this function:

Distalheatmap <- plotEnrichHeatmap( seEnrich = enrichMotifs[,1], pal = paletteContinuous(set = "comet", n = 100), n = 10, cutOff = 20, pMax = Inf, clusterCols = TRUE, binaryClusterRows = TRUE, labelRows = TRUE, rastr = TRUE, transpose = FALSE, returnMatrix = FALSE, logFile = createLogFile("plotEnrichHeatmap") )

but is there a groupBy parameter such that I could separate the samples in this integrated dataset?

Thanks!