ssvSignalClustering {seqsetvis} | R Documentation |
clustering as for a heatmap
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)
bw_data |
a GRanges or data.table of bigwig signal.
As returned from |
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 |
data.table of signal profiles, ready for ssvSignalHeatmap
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)