merge_clusters {seqsetvis} | R Documentation |
merge_clusters
merge_clusters( clust_dt, to_merge, row_ = "id", cluster_ = "cluster_id", reapply_cluster_names = TRUE )
clust_dt |
data.table output from |
to_merge |
Clusters to merge. Must be items in clust_dt variable defined by cluster_ parameter. |
row_ |
variable name mapped to row, likely id or gene name for ngs data. Default is "id" and works with ssvFetch* output. |
cluster_ |
variable name to use for cluster info. Default is "cluster_id". |
reapply_cluster_names |
If TRUE, clusters will be renamed according to new order instead of their original names. Default is TRUE. |
data.table as output from ssvSignalClustering
set.seed(0) clust_dt = ssvSignalClustering(CTCF_in_10a_profiles_dt, nclust = 6) ssvSignalHeatmap(clust_dt) agg_dt = clust_dt[, list(y = mean(y)), list(x, cluster_id, sample)] ggplot(agg_dt, aes(x = x, y = y, color = sample)) + geom_path() + facet_grid(cluster_id~.) to_merge = c(2, 3, 5) # debug(merge_clusters) new_dt = merge_clusters(clust_dt, c(2, 3, 5), reapply_cluster_names = FALSE) new_dt.relabel = merge_clusters(clust_dt, c(2, 3, 5), reapply_cluster_names = TRUE) new_dt.relabel.sort = within_clust_sort(new_dt.relabel, within_order_strategy = "sort") table(clust_dt$cluster_id) table(new_dt$cluster_id) cowplot::plot_grid( ssvSignalHeatmap(clust_dt) + labs(title = "original"), ssvSignalHeatmap(new_dt) + labs(title = "2,3,5 merged"), ssvSignalHeatmap(new_dt.relabel) + labs(title = "2,3,5 merged, renumbered"), ssvSignalHeatmap(new_dt.relabel.sort) + labs(title = "2,3,5 merged, renumbered and sorted") )