reverse_clusters: reverse_clusters

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

reverse_clusters

Description

reverse_clusters

Usage

reverse_clusters(
  clust_dt,
  row_ = "id",
  column_ = "x",
  fill_ = "y",
  facet_ = "sample",
  cluster_ = "cluster_id",
  reverse_rows_within = TRUE,
  reapply_cluster_names = TRUE
)

Arguments

clust_dt	data.table output from ssvSignalClustering
row_	variable name mapped to row, likely id or gene name for ngs data. Default is "id" and works with ssvFetch* output.
column_	varaible mapped to column, likely bp position for ngs data. Default is "x" and works with ssvFetch* output.
fill_	numeric variable to map to fill. Default is "y" and works with ssvFetch* output.
facet_	variable name to facet horizontally by. Default is "sample" and works with ssvFetch* output. Set to "" if data is not facetted.
cluster_	variable name to use for cluster info. Default is "cluster_id".
reverse_rows_within	If TRUE, rows within clusters will be reversed as well. Default is TRUE.
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 = 3)
rev_dt = reverse_clusters(clust_dt)
rev_dt.no_relabel = reverse_clusters(clust_dt, reapply_cluster_names = FALSE)
rev_dt.not_rows = reverse_clusters(clust_dt, reverse_rows_within = FALSE)
cowplot::plot_grid(nrow = 1,
  ssvSignalHeatmap(clust_dt) + labs(title = "original"),
  ssvSignalHeatmap(rev_dt) + labs(title = "reversed"),
  ssvSignalHeatmap(rev_dt.no_relabel) + labs(title = "reversed, no relabel"),
  ssvSignalHeatmap(rev_dt.not_rows) + labs(title = "reversed, not rows")
)

jrboyd/seqsetvis documentation built on Oct. 15, 2024, 11:28 p.m.