ssvSignalClustering {seqsetvis}R Documentation

clustering as for a heatmap

Description

clustering as for a heatmap

Usage

ssvSignalClustering(bw_data, nclust = 6, row_ = "id", column_ = "x",
  fill_ = "y", facet_ = "sample", cluster_ = "cluster_id",
  max_rows = 500, max_cols = 100, clustering_col_min = -Inf,
  clustering_col_max = Inf)

Arguments

bw_data

a GRanges or data.table of bigwig signal. As returned from ssvFetchBam and ssvFetchBigwig

nclust

number of clusters

row_

variable name mapped to row, likely peak id or gene name for ngs data

column_

varaible mapped to column, likely bp position for ngs data

fill_

numeric variable to map to fill

facet_

variable name to facet horizontally by

cluster_

variable name to use for cluster info

max_rows

for speed rows are sampled to 500 by default, use Inf to plot full data

max_cols

for speed columns are sampled to 100 by default, use Inf to plot full data

clustering_col_min

numeric minimum for col range considered when clustering, default in -Inf

clustering_col_max

numeric maximum for col range considered when clustering, default in Inf

Value

data.table of signal profiles, ready for ssvSignalHeatmap

Examples

clust_dt = ssvSignalClustering(CTCF_in_10a_profiles_gr)
ssvSignalHeatmap(clust_dt)

clust_dt2 = ssvSignalClustering(CTCF_in_10a_profiles_gr, nclust = 2)
ssvSignalHeatmap(clust_dt2)

#clustering can be targetted to a specific part of the region
clust_dt3 = ssvSignalClustering(CTCF_in_10a_profiles_gr, nclust = 2,
    clustering_col_min = -250, clustering_col_max = -150)
ssvSignalHeatmap(clust_dt3)
clust_dt4 = ssvSignalClustering(CTCF_in_10a_profiles_gr, nclust = 2,
    clustering_col_min = 150, clustering_col_max = 250)
ssvSignalHeatmap(clust_dt4)

[Package seqsetvis version 1.0.2 Index]