Man pages for xiangpin/MicrobitaProcess
an R package for analysis, visualization and biomarker discovery of microbiome

alphasample-classalphasample class
as.data.frameget the table of diffAnalysisClass
as.treedataas.treedata
build_treebuilding tree
clustplotClass-classclustplotClass class
convert_to_treedataconvert dataframe contained hierarchical relationship or...
data-hmp_aerobiosis_small(Data) Small subset of the HMP 16S dataset
data-kostic2012crc(Data) Genomic analysis identifies association of...
data-test_otu_data(Data) simulated dataset.
diff_analysisDifferential expression analysis
diffAnalysisClass-classdiffAnalysisClass class
drop_taxaDropping Species with Few abundance and Few Occurrences
generalizedFCgeneralized fold change
geom_ord_ellipseadd confidence ellipse to ordinary plot
get_alltaxadfget the table of abundance of all level taxonomy
get_alphaindexalpha index
get_clustHierarchical cluster analysis for the samples
get_coordget ordination coordinates.
get_countcalculate the count or relative abundance of replicate...
get_distcalculate distance
get_mean_medianget the mean and median of specific feature.
get_pcaPerforms a principal components analysis
get_pcoaperforms principal coordinate analysis (PCoA)
get_pvalueMethods for computation of the p-value
get_rarecurveobtain the result of rare curve
get_sampledflistGenerate random data list from a original data.
get_taxadfget the data of specified taxonomy
get_upsetgenerate the dataset for upset of UpSetR
get_varctget the contribution of variables
get_vennlistgenerate a vennlist for VennDiagram
ggbartaxtaxonomy barplot
ggboxA box or violin plot with significance test
ggclustplot the result of hierarchical cluster analysis for the...
ggdiffboxboxplot for the result of diff_analysis
ggdiffcladeplot the clade tree with highlight
ggdifftaxbarsignificantly discriminative feature barplot
ggeffectsizevisualization of effect size by the Linear Discriminant...
ggordpointordination plotter based on ggplot2.
ggrarecurveRarefaction alpha index
import_dada2Import function to load the feature table and taxanomy table...
import_qiime2Import function to load the output of qiime2.
mappingtaxdagenerate the mapping data
multi_comparea container for performing two or more sample test.
ordplotClass-classordplotClass class
pcasample-classpcasample class
pcoa-classpcoa class
prcomp-classprcomp class
read_qzaread the qza file, output of qiime2.
reexportsObjects exported from other packages
show-methodsmethod extensions to show for diffAnalysisClass objects.
split_dataSplit Large Vector or DataFrame
split_str_to_listsplit a dataframe contained one column
stat_raremapping data of ggrarecurve
theme_taxbartheme_taxbar
xiangpin/MicrobitaProcess documentation built on Feb. 8, 2021, 4:39 p.m.