MakeHeatmapData: Prepare agglomerated dataframe for heatmap display.

In eclarke/eclectic: Miscellaneous functions for bioinformatics data

Description

Aggregates counts by minimum rank, completing missing cases, and clustering rows. Expects input agg to have columns called SampleID and count at minimum.

Usage

MakeHeatmapData(agg, s, min.rank.1 = "Genus", min.rank.2 = NA,
  min.samples = 1, hclust_method = "average", ...)

Arguments

agg	an agglomerated df from agglomerate.
s	sample metadata dataframe
min.rank.1	the most specific rank to aggregate by (determines y-axis) Uses min_rank to select next most specific rank if not available.
min.rank.2	(optional) higher rank to prefix min.rank.1 (e.g. Phylum) Uses min_rank to select next most specific rank if not available.
min.samples	a row must appear more in than this number of samples to be shown
hclust_method	a character vector specifying the method to use for clustering y-axis (from hclust)
...	additional samples passed to the min_rank calls

eclarke/eclectic documentation built on May 15, 2019, 7:54 p.m.