ssvSignalClustering: clustering as for a heatmap

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

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,
  within_order_strategy = c("hclust", "sort")[2],
  dcast_fill = NA
)

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
within_order_strategy	one of "hclust" or "sort". if hclust, hierarchical clustering will be used. if sort, a simple decreasing sort of rosSums.
dcast_fill	value to supply to dcast fill argument. default is NA.

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)

seqsetvis documentation built on Nov. 8, 2020, 5:57 p.m.