MakeHeatmapData: Prepare agglomerated dataframe for heatmap display by...

In eclarke/sarcoid-microbiome-paper: Figures for the Clarke et al sarcoid microbiome paper

Description

Prepare agglomerated dataframe for heatmap display by aggregating counts by minimum rank, completing missing cases, and clustering rows

Usage

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

Arguments

s	sample metadata dataframe
min.rank.1	the most specific rank to aggregate by (determines y-axis) Uses tax_climber to select next most specific rank if not available.
min.rank.2	(optional) higher rank to prefix min.rank.1 (e.g. Phylum) Uses tax_climber to select next most specific rank if not available.
min.samples	the minimum number of samples required for a taxa to appear
min.samples	a row must appear more than this number of samples to be shown

eclarke/sarcoid-microbiome-paper documentation built on May 29, 2019, 2:52 p.m.