reorder_clusters_stepdown {seqsetvis} | R Documentation

## 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

    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)
    )

[Package seqsetvis version 1.14.4 Index]