pf.heatmap: Heatmap for phylofactor data

In reptalex/phylofactor: phylofactor

Heatmap for phylofactor data

Description

Heatmap for phylofactor data

Usage

pf.heatmap(PF = NULL, tree = NULL, Data = NULL, factors = NULL,
  column.order = NULL, branch.length = "none", color = NA,
  font.size = 0, ...)

Arguments

PF	phylofactor class object from either PhyloFactor or gpf with algorithm='mStable'
tree	optional input, only used if PF is not input. If inputting tree, must also input Data
Data	Dataset with rows equal to the number of species. Ideally, rownames are all equal to PF$tree of tree tip-labels. Otherwise, rows must be in order of tree tip-labels.
factors	vector of integer factors for input with PF. Will use pf.tree to highlight clades obtained at each factor.
column.order	vector of integers of length equal to ncol(Data) or ncol(PF$Data). Will re-order the data (e.g. according to desired meta-data).
branch.length	input for ggtree
color	input color for gheatmap
font.size	font size for gheatmap
...	additional arguments passed to gheatmap

Examples

library(phylofactor)
require(ggpubr)
data(FTmicrobiome)
PF <- FTmicrobiome$PF
obs <- PF$transform.fcn(PF$Data)
pred <- predict(PF,factor=3)
observed <- pf.heatmap(PF,Data=obs,factors=1:3,width=3)
predicted <- pf.heatmap(PF,Data=pred,factors=1:3,width=3)
ggarrange(observed,predicted,nrow=2)

reptalex/phylofactor documentation built on Feb. 28, 2024, 3:19 p.m.