reorder_clusters_stepdown: reorder_clusters_stepdown

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

reorder_clusters_stepdown

Description

Attempts to reorder clusters so that rows with highest signal on the left relative to the right appear at the top. Signal should have a roughly diagonal pattern in a "stepdown" pattern.

Usage

reorder_clusters_stepdown(
  clust_dt,
  row_ = "id",
  column_ = "x",
  fill_ = "y",
  facet_ = "sample",
  cluster_ = "cluster_id",
  reapply_cluster_names = TRUE,
  step_by_column = TRUE,
  step_by_facet = FALSE
)

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".
reapply_cluster_names	If TRUE, clusters will be renamed according to new order instead of their original names. Default is TRUE.
step_by_column	If TRUE, column is considered for left-right cluster balance. Default is TRUE.
step_by_facet	If TRUE, facet is considered for left-right cluster balance. Default is FALSE.

Details

This can be down by column (step_by_column = TRUE) which averages across facets. By facet (step_by_column = FALSE, step_by_facet = TRUE) which averages all columns per facet. Or both column and facet (step_by_column = TRUE, step_by_facet = TRUE), which does no averaging so it looks at the full matrix as plotted.

Value

data.table as output from ssvSignalClustering

Examples

data(CTCF_in_10a_profiles_dt)
clust_dt = ssvSignalClustering(CTCF_in_10a_profiles_dt, nclust = 10)
new_dt = reorder_clusters_stepdown(clust_dt)
cowplot::plot_grid(
    ssvSignalHeatmap(clust_dt),
    ssvSignalHeatmap(new_dt)
)

jrboyd/seqsetvis documentation built on Jan. 16, 2025, 10:25 a.m.