extract order of clustered column

[chrismahony]

I have created my pheatmap using:

p<-pheatmap(mat),
scale = "row",
show_rownames = T, show_colnames = T,
border_color = NA,
clustering_method = "average",
clustering_distance_rows = "correlation",
clustering_distance_cols = "correlation",
breaks = seq(-3, 3, 0.05),
color = colorRampPalette(c("purple3", "black", "yellow2"))(120),
annotation_col =
pData(target_demoData)[, c("Annotation_initial2", "Conditon2")] )
p

How can I extract the clustering order of the column of my samples? Essentially I have >100 samples and pheatmap nicely clusters them in to 2 broad groups, how can I extract the plotting order for downstream analysis?

When I examine p there does not seem to be this data in the object,
thanks

[AlexWeinreb]

As ?pheatmap indicates in the "Value" section, p contains a list with a component tree_row, which is "the clustering of rows as hclust object". You can get more details in the "Value" section of ?hclust, notably:

order
a vector giving the permutation of the original observations suitable for plotting, in the sense that a cluster plot using this ordering and matrix merge will not have crossings of the branches.

So the exact order is available with:

p$tree_col$order

or if you want the labels in their clustered order:

p$tree_col$labels[p$tree_col$order]