ggclust: plot the result of hierarchical cluster analysis for the...

In MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome

Description

plot the result of hierarchical cluster analysis for the samples

Usage

ggclust(obj, ...)

## S3 method for class 'clustplotClass'
ggclust(
  obj,
  layout = "rectangular",
  factorNames = NULL,
  factorLevels = NULL,
  pointsize = 2,
  fontsize = 2.6,
  hjust = -0.1,
  settheme = TRUE,
  ...
)

Arguments

obj	R object, clustplotClass.
...,	additional params, see also geom_tippoint
layout	character, the layout of tree, see also ggtree.
factorNames	character, default is NULL.
factorLevels	list, default is NULL.
pointsize	numeric, the size of point, default is 2.
fontsize	numeric, the size of text of tiplabel, default is 2.6.
hjust	numeric, default is -0.1
settheme	logical, default is TRUE.

Value

the figures of hierarchical cluster.

Author(s)

Shuangbin Xu

Examples

#don't run in examples
#library(phyloseq)
#library(ggtree)
#library(ggplot2)
#data(GlobalPatterns)
#subGlobal <- subset_samples(GlobalPatterns,
#         SampleType %in% c("Feces", "Mock", "Ocean", "Skin"))
#hcsample <- get_clust(subGlobal, distmethod="jaccard",
#                  method="hellinger", hclustmethod="average")
#hc_p <- ggclust(hcsample, layout = "rectangular",
#                pointsize=1, fontsize=0,
#                factorNames=c("SampleType")) +
#        theme_tree2(legend.position="right",
#                    plot.title = element_text(face="bold", lineheight=25,hjust=0.5))

MicrobiotaProcess documentation built on April 18, 2021, 6 p.m.