merge_clusters: merge_clusters

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

merge_clusters

Description

merge_clusters

Usage

merge_clusters(
  clust_dt,
  to_merge,
  row_ = "id",
  cluster_ = "cluster_id",
  reapply_cluster_names = TRUE
)

Arguments

clust_dt	data.table output from ssvSignalClustering
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.

Value

data.table as output from ssvSignalClustering

Examples

data(CTCF_in_10a_profiles_dt)
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")
)

jrboyd/seqsetvis documentation built on Dec. 10, 2024, 11:23 a.m.