make_clustering_matrix: make_clustering_matrix

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

make_clustering_matrix

Description

Create a wide matrix from a tidy data.table more suitable for clustering methods

Usage

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,
  fun.aggregate = "mean"
)

Arguments

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.
fun.aggregate	Function to aggregate when multiple values present for facet_, row_, and column_. The function should accept a single vector argument or be a character string naming such a function.

Value

A wide matrix version of input tidy data.table

Examples

data(CTCF_in_10a_profiles_dt)
mat = make_clustering_matrix(CTCF_in_10a_profiles_dt)
mat[1:5, 1:5]

jrboyd/seqsetvis documentation built on Dec. 10, 2024, 11:23 a.m.