ggdifftaxbar: significantly discriminative feature barplot

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

Description

significantly discriminative feature barplot

Usage

ggdifftaxbar(obj, ...)

ggdiffbartaxa(obj, ...)

## S4 method for signature 'diffAnalysisClass'
ggdifftaxbar(
  obj,
  filepath = NULL,
  output = "biomarker_barplot",
  removeUnknown = TRUE,
  figwidth = 6,
  figheight = 3,
  ylabel = "relative abundance",
  format = "pdf",
  dpi = 300,
  ...
)

## S3 method for class 'featureMeanMedian'
ggdifftaxbar(
  obj,
  featurename,
  classgroup,
  subclass,
  xtextsize = 3,
  factorLevels = NULL,
  coloslist = NULL,
  ylabel = "relative abundance",
  ...
)

Arguments

obj	object, diffAnalysisClass see also diff_analysis or feMeanMedian class, see also get_mean_median.
...	additional arguments.
filepath	character, default is NULL, meaning current path.
output	character, the output dir name, default is "biomarker_barplot".
removeUnknown	logical, whether do not show unknown taxonomy, default is TRUE.
figwidth	numeric, the width of figures, default is 6.
figheight	numeric, the height of figures, default is 3.
ylabel	character, the label of y, default is 'relative abundance'.
format	character, the format of figure, default is pdf, png, tiff also be supported.
dpi	numeric, the dpi of output, default is 300.
featurename	character, the feature name, contained at the objet.
classgroup	character, factor name.
subclass	character, factor name.
xtextsize	numeric, the size of axis x label, default is 3.
factorLevels	list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this.
coloslist	vector, color vector, if the input is phyloseq, you should use this to adjust the color, not scale_color_manual.

Value

the figures of features show the distributions in samples.

Author(s)

Shuangbin Xu

Examples

data(kostic2012crc)
kostic2012crc
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)
# not run in example
#ggdifftaxbar(diffres, output="biomarker_barplot")

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