make_clustering_matrix {seqsetvis} | R Documentation |
Create a wide matrix from a tidy data.table more suitable for clustering methods
make_clustering_matrix( tidy_dt, row_ = "id", column_ = "x", fill_ = "y", facet_ = "sample", max_rows = 500, max_cols = 100, clustering_col_min = -Inf, clustering_col_max = Inf, dcast_fill = NA )
tidy_dt |
the tidy data.table to covert to a wide matrix. Must have entries for variables specified by row_, column_, fill_, and facet_. |
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 |
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 |
dcast_fill |
value to supply to dcast fill argument. default is NA. |
A wide matrix version of input tidy data.table
mat = make_clustering_matrix(CTCF_in_10a_profiles_dt) mat[1:5, 1:5]