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

alphasample-classalphasample class
as.MPSEas.MPSE method
as.phyloseqconvert to phyloseq object.
build_treebuilding tree
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
dr_extractExtracting the internal tbl_df attribute of tibble.
drop_taxaDropping Species with Few abundance and Few Occurrences
extract_binary_offspringextract the binary offspring of the specified internal nodes
generalizedFCgeneralized fold change
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_NRI_NTI-methodscalculating related phylogenetic alpha metric
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
ImportDada2Import function to load the feature table and taxonomy table...
ImportQiime2Import function to load the output of qiime2.
mouse.time.mpse(Data) An example data
mp_adonis-methodsPermutational Multivariate Analysis of Variance Using...
mp_aggregate_clade-methodscalculate the mean/median (relative) abundance of internal...
mp_aggregate-methodsaggregate the assays with the specific group of sample and...
mp_anosim-methodsAnalysis of Similarities (ANOSIM) with MPSE or tbl_mpse...
mp_balance_clade-methodsCalculating the balance score of internal nodes (clade)...
mp_cal_abundance-methodsCalculate the (relative) abundance of each taxonomy class for...
mp_cal_alpha-methodscalculate the alpha index with MPSE or tbl_mpse
mp_cal_cca-methods[Partial] [Constrained] Correspondence Analysis with MPSE or...
mp_cal_clust-methodsHierarchical cluster analysis for the samples with MPSE or...
mp_cal_dca-methodsDetrended Correspondence Analysis with MPSE or tbl_mpse...
mp_cal_dist-methodsCalculate the distances between the samples or features with...
mp_cal_divergence-methodscalculate the divergence with MPSE or tbl_mpse
mp_cal_nmds-methodsNonmetric Multidimensional Scaling Analysis with MPSE or...
mp_cal_pca-methodsPrincipal Components Analysis with MPSE or tbl_mpse object
mp_cal_pcoa-methodsPrincipal Coordinate Analysis with MPSE or tbl_mpse object
mp_cal_pd_metric-methodsCalculating related phylogenetic alpha metric with MPSE or...
mp_cal_rarecurve-methodsCalculating the different alpha diversities index with...
mp_cal_rda-methods[Partial] [Constrained] Redundancy Analysis with MPSE or...
mp_cal_upset-methodsCalculating the samples or groups for each OTU, the result...
mp_cal_venn-methodsCalculating the OTU for each sample or group, the result can...
mp_decostand-methodsThis Function Provideds Several Standardization Methods for...
mp_diff_analysis-methodsDifferential expression analysis for MPSE or tbl_mpse object
mp_diff_clade-methodsDifferential internal and tip nodes (clades) analysis for...
mp_dmngroup-methodsDirichlet-Multinomial generative classifiers to MPSE or...
mp_dmn-methodsFit Dirichlet-Multinomial models to MPSE or tbl_mpse
mp_envfit-methodsFits an Environmental Vector or Factor onto an Ordination...
mp_extract_abundance-methodsExtracting the abundance metric from MPSE or tbl_mpse object
mp_extract_assays-methodsextract the abundance matrix from MPSE object or tbl_mpse...
mp_extract_dist-methodsextract the dist object from MPSE or tbl_mpse object
mp_extract_feature-methodsextract the feature (OTU) information in MPSE object
mp_extract_internal_attr-methodsExtracting the PCA, PCoA, etc results from MPSE or tbl_mpse...
mp_extract_rarecurve-methodsExtract the result of mp_cal_rarecurve with action="add" from...
mp_extract_refseq-methodsExtract the representative sequences from MPSE object
mp_extract_sample-methodsextract the sample information in MPSE object
mp_extract_taxonomy-methodsextract the taxonomy annotation in MPSE object
mp_extract_tree-methodsextract the taxonomy tree in MPSE object
mp_filter_taxa-methodsFilter OTU (Features) By Abundance Level
mp_import_biombuilding MPSE object from biom-format file.
mp_import_metaphlanImport function to load the output of MetaPhlAn.
mp_import_qiimeImport function to load the output of qiime.
mp_mantel-methodsMantel and Partial Mantel Tests for MPSE or tbl_mpse Object
mp_mrpp-methodsAnalysis of Multi Response Permutation Procedure (MRPP) with...
mp_plot_abundance-methodsplotting the abundance of taxa via specified taxonomy class
mp_plot_alpha-methodsPlotting the alpha diversity between samples or groups.
mp_plot_diff_boxplot-methodsdisplaying the differential result contained abundance and...
mp_plot_diff_cladogramVisualizing the result of mp_diff_analysis with cladogram.
mp_plot_diff_res-methodsThe visualization of result of mp_diff_analysis
mp_plot_dist-methodsPlotting the distance between the samples with heatmap or...
mp_plot_ord-methodsPlotting the result of PCA, PCoA, CCA, RDA, NDMS or DCA
mp_plot_rarecurve-methodsRarefaction alpha index with MPSE
mp_plot_upset-methodsPlotting the different number of OTU between group via UpSet...
mp_plot_venn-methodsPlotting the different number of OTU between groups with Venn...
mp_rrarefy-methodsmp_rrarefy method
MPSEConstruct a MPSE object
MPSE-accessorsMPSE accessors
MPSE-classMPSE class
mp_select_as_tip-methodsselect specific taxa level as rownames of MPSE
mp_stat_taxa-methodsCount the number and total number taxa for each sample at...
multi_comparea container for performing two or more sample test.
ordplotClass-classordplotClass class
pcasample-classpcasample class
pcoa-classpcoa class
prcomp-classprcomp class
printprint some objects
read_qzaread the qza file, output of qiime2.
reexportsObjects exported from other packages
scale_fill_diff_cladogramCreate the scale of mp_plot_diff_cladogram.
set_diff_boxplot_colorset the color scale of plot generated by mp_plot_diff_boxplot
set_scale_themeadjust the color of heatmap of mp_plot_dist
show-methodsmethod extensions to show for diffAnalysisClass or...
split_dataSplit Large Vector or DataFrame
split_str_to_listsplit a dataframe contained one column
theme_stampset the theme of ggplot object with the STAMP style.
xiangpin/MicrobitaProcess documentation built on Oct. 4, 2022, 6:28 a.m.