R/platjam-import.R
get_nmat_ceiling.RdHelper function to calculate signal ceiling of numeric matrix
get_nmat_ceiling(imat, iceiling = NULL, verbose = TRUE, ...)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)
using only non-zero values
otherwise iceiling is used as a 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.
Other jam coverage heatmap functions:
coverage_matrix2nmat(),
nmathm_row_order(),
nmatlist2heatmaps(),
validate_heatmap_params(),
zoom_nmatlist(),
zoom_nmat()