get_nmat_ceiling: Helper function to calculate signal ceiling of numeric matrix

In jmw86069/platjam: Platform Jam, biological platform importers.

Helper function to calculate signal ceiling of numeric matrix

Description

Helper function to calculate signal ceiling of numeric matrix

Usage

get_nmat_ceiling(imat, iceiling = NULL, verbose = TRUE, ...)

Details

This function is called by nmatlist2heatmaps() and is not intended to be called directly.

It takes a normalizedMatrix or numeric matrix object, and a ceiling value iceiling and determines an appropriate numeric ceiling with the following rules:

• if iceiling is NULL, it returns the highest absolute value in imat

• if iceiling > 0 and iceiling <= 1, it calculates quantile(abs(imat), probs=iceiline), excluding values of zero

• otherwise iceiling is used as a fixed numerical ceiling

In all cases, iceiling is rounded to 3 digits with round(iceiling, digits=3)

Also in all cases, na.rm=TRUE is used, to prevent returning NA.

See Also

Other jam coverage heatmap functions: coverage_matrix2nmat(), nmathm_row_order(), nmatlist2heatmaps(), recenter_nmatlist(), restrand_nmatlist(), validate_heatmap_params(), zoom_nmatlist(), zoom_nmat()

jmw86069/platjam documentation built on Sept. 26, 2024, 3:31 p.m.