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

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

plot the result of hierarchical cluster analysis for the samples

Description

plot the result of hierarchical cluster analysis for the samples

Usage

ggclust(obj, ...)

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

Arguments

obj	R object, treedata object.
...	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

Value

the figures of hierarchical cluster.

Author(s)

Shuangbin Xu

Examples

## Not run: 
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))

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.