ggdiffclade: plot the clade tree with highlight

In xiangpin/MicrobitaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

plot the clade tree with highlight

Description

plot results of different analysis or data.frame, contained hierarchical relationship or other classes,such like the tax_data of phyloseq.

Usage

ggdiffclade(obj, ...)

## S3 method for class 'data.frame'
ggdiffclade(
  obj,
  nodedf,
  factorName,
  size,
  layout = "radial",
  linewd = 0.6,
  bg.tree.color = "#bed0d1",
  bg.point.color = "#bed0d1",
  bg.point.stroke = 0.2,
  bg.point.fill = "white",
  skpointsize = 2,
  hilight.size = 0.2,
  alpha = 0.4,
  taxlevel = 5,
  cladetext = 2.5,
  tip.annot = TRUE,
  as.tiplab = TRUE,
  factorLevels = NULL,
  xlim = 12,
  removeUnknown = FALSE,
  reduce = FALSE,
  type = "species",
  ...
)

## S3 method for class 'diffAnalysisClass'
ggdiffclade(obj, size, removeUnknown = TRUE, ...)

Arguments

obj	object, diffAnalysisClass, the results of diff_analysis see also diff_analysis, or data.frame, contained hierarchical relationship or other classes.
...	additional parameters.
nodedf	data.frame, contained the tax and the factor information and(or pvalue).
factorName	character, the names of factor in nodedf.
size	the column name for mapping the size of points, default is 'pvalue'.
layout	character, the layout of ggtree, but only "rectangular", "roundrect", "ellipse", "radial", "slanted", "inward_circular" and "circular" in here, default is "radial".
linewd	numeric, the size of segment of ggtree, default is 0.6.
bg.tree.color	character, the line color of tree, default is '#bed0d1'.
bg.point.color	character, the color of margin of background node points of tree, default is '#bed0d1'.
bg.point.stroke	numeric, the margin thickness of point of background nodes of tree, default is 0.2 .
bg.point.fill	character, the point fill (since point shape is 21) of background nodes of tree, default is 'white'.
skpointsize	numeric, the point size of skeleton of tree, default is 2.
hilight.size	numeric, the margin thickness of high light clade, default is 0.2.
alpha	numeric, the alpha of clade, default is 0.4.
taxlevel	positive integer, the full text of clade, default is 5.
cladetext	numeric, the size of text of clade, default is 2.
tip.annot	logcial whether to replace the differential tip labels with shorthand, default is TRUE.
as.tiplab	logical, whether to display the differential tip labels with 'geom_tiplab' of 'ggtree', default is TRUE, if it is FALSE, it will use 'geom_text_repel' of 'ggrepel'.
factorLevels	list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this.
xlim	numeric, the x limits, only works for 'inward_circular' layout, default is 12.
removeUnknown	logical, whether do not show unknown taxonomy, default is TRUE.
reduce	logical, whether remove the unassigned taxonomy, which will remove the clade of unassigned taxonomy, but the result of 'diff_analysis' should remove the unknown taxonomy, default is FALSE.
type	character, the type of datasets, default is "species", if the dataset is not about species, such as dataset of kegg function, you should set it to "others".

Value

figures of tax clade show the significant different feature.

Author(s)

Shuangbin Xu

Examples

## Not run: 
data(kostic2012crc)
kostic2012crc %<>% as.phyloseq()
head(phyloseq::sample_data(kostic2012crc),3)
kostic2012crc <- phyloseq::rarefy_even_depth(kostic2012crc,
                         rngseed=1024)
table(phyloseq::sample_data(kostic2012crc)$DIAGNOSIS)
set.seed(1024)
diffres <- diff_analysis(kostic2012crc, classgroup="DIAGNOSIS",
                        mlfun="lda", filtermod="fdr",
                        firstcomfun = "kruskal.test",
                        firstalpha=0.05, strictmod=TRUE,
                        secondcomfun = "wilcox.test",
                        subclmin=3, subclwilc=TRUE,
                        secondalpha=0.01, ldascore=3)
library(ggplot2)
diffcladeplot <- ggdiffclade(diffres,alpha=0.3, linewd=0.2, 
                        skpointsize=0.4, 
                        taxlevel=5) +
                 scale_fill_diff_cladogram(
                        values=c('#00AED7', 
                                 '#FD9347'
                                 )
                 ) +
                 scale_size_continuous(range = c(1, 3))

## End(Not run)

xiangpin/MicrobitaProcess documentation built on Nov. 6, 2024, 1:15 a.m.