1. Anatomy of a MPSE | 2. Overview of the design of MicrobiotaProcess package | 3. MicrobiotaProcess profiling | 3.1 bridges other tools | 3.2 alpha diversity analysis | 3.3 calculate alpha index and visualization | 3.4 The visualization of taxonomy abundance | 3.5 Beta diversity analysis | 3.5.1 The distance between samples or groups | 3.5.2 The PCoA analysis | 3.5.3 Hierarchical cluster analysis | 3.6 Biomarker discovery | 4. Need helps? | 5. Session information | 6. References
Package: MicrobiotaProcess 1.25.0
Shuangbin Xu
MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework).
Authors:
MicrobiotaProcess_1.25.0.tar.gz
MicrobiotaProcess_1.25.0.zip(r-4.7)MicrobiotaProcess_1.25.0.zip(r-4.6)MicrobiotaProcess_1.25.0.zip(r-4.5)
MicrobiotaProcess_1.25.0.tgz(r-4.6-any)MicrobiotaProcess_1.25.0.tgz(r-4.5-any)
MicrobiotaProcess_1.25.0.tar.gz(r-4.7-any)MicrobiotaProcess_1.25.0.tar.gz(r-4.6-any)
MicrobiotaProcess_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MicrobiotaProcess/json (API)
| # Install 'MicrobiotaProcess' in R: |
| install.packages('MicrobiotaProcess', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yulab-smu/microbiotaprocess/issues
Datasets:
- kostic2012crc -
- mouse.time.mpse - (Data) An example data
- test_otu_data - (Data) simulated dataset.
On BioConductor:MicrobiotaProcess-1.25.0(bioc 3.24)MicrobiotaProcess-1.24.0(bioc 3.23)
visualizationmicrobiomesoftwaremultiplecomparisonfeatureextractionmicrobiome-analysismicrobiome-data
Last updated from:29492fac06. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 241 | ||
| linux-devel-x86_64 | NOTE | 464 | ||
| source / vignettes | OK | 346 | ||
| linux-release-x86_64 | NOTE | 445 | ||
| macos-release-arm64 | NOTE | 345 | ||
| macos-oldrel-arm64 | NOTE | 294 | ||
| windows-devel | NOTE | 330 | ||
| windows-release | NOTE | 365 | ||
| windows-oldrel | NOTE | 303 | ||
| wasm-release | OK | 171 |
Exports:%<>%%>%arrangeas_phyloseqas_tibbleas.mpseas.MPSEas.phyloseqas.treedatabuild_treecolDatacolData<-convert_to_treedatadiff_analysisdistinctdr_extractdrop_taxaextractextract_binary_offspringfilterfortifygeneralizedFCget_alltaxadfget_alphaindexget_clustget_coordget_countget_distget_mean_medianget_NRI_NTIget_pcaget_pcoaget_pvalueget_rarecurveget_ratioget_sampledflistget_taxadfget_upsetget_varctget_vennlistggbartaxggbartaxaggboxggclustggdiffbartaxaggdiffboxggdiffcladeggdifftaxbarggeffectsizeggordpointggrarecurvegroup_byimport_dada2import_qiime2left_joinmp_adonismp_aggregatemp_aggregate_clademp_anosimmp_balance_clademp_cal_abundancemp_cal_alphamp_cal_ccamp_cal_clustmp_cal_dcamp_cal_distmp_cal_divergencemp_cal_nmdsmp_cal_pcamp_cal_pcoamp_cal_pd_metricmp_cal_rarecurvemp_cal_rdamp_cal_upsetmp_cal_vennmp_decostandmp_diff_analysismp_diff_clademp_dmnmp_dmngroupmp_envfitmp_extract_abundancemp_extract_assaysmp_extract_distmp_extract_featuremp_extract_internal_attrmp_extract_otutreemp_extract_rarecurvemp_extract_refseqmp_extract_samplemp_extract_taxatreemp_extract_taxonomymp_extract_treemp_filter_taxamp_fortifymp_import_biommp_import_dada2mp_import_humann_regroupmp_import_metaphlanmp_import_qiimemp_import_qiime2mp_mantelmp_mrppmp_plot_abundancemp_plot_alphamp_plot_diff_boxplotmp_plot_diff_cladogrammp_plot_diff_manhattanmp_plot_diff_resmp_plot_distmp_plot_ordmp_plot_rarecurvemp_plot_upsetmp_plot_vennmp_rrarefymp_select_as_tipmp_stat_taxaMPSEmulti_comparemutatenestotutreeotutree<-pullread_qzarefsequencerefsequence<-remove_missingrenamerowDatarownames<-scale_fill_diff_cladogramselectset_diff_boxplot_colorset_scale_themeshowslicesplit_datasplit_str_to_listtax_tabletaxatreetaxatree<-taxonomytaxonomy<-td_filtertd_unnesttheme_taxbarungroupunnest
Dependencies:abindapeaplotbase64encBiobaseBiocGenericsBiostringsbslibcachemcliclustercodetoolscoincpp11crayondata.tableDelayedArraydigestdplyrdtplyrevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforeachfsgdtoolsgenericsGenomicRangesggfunggiraphggnewscaleggplot2ggplotifyggrepelggsignifggstarggtreeggtreeExtragluegridExtragridGraphicsgtablehighrhtmltoolshtmlwidgetsIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglatticelazyevallibcoinlifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemodeltoolsmultcompmvtnormnlmepatchworkpermutepillarpkgconfigplyrpurrrR6rappdirsRColorBrewerRcpprlangrmarkdownS4ArraysS4VectorsS7sandwichsassscalesSeqinfoSparseArraystringistringrSummarizedExperimentsurvivalsystemfontsTH.datatibbletidyrtidyselecttidytreetinytextreeioutf8vctrsveganviridisLitewithrxfunXVectoryamlyulab.utilszoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| alphasample class | alphasample-class |
| as.MPSE method | as.MPSE as.mpse |
| convert to phyloseq object. | as.phyloseq as.phyloseq.MPSE as.phyloseq.tbl_mpse as_phyloseq |
| as.treedata | as.treedata.taxonomyTable |
| building tree | build_tree build_tree,character build_tree,character-method build_tree,DNAbin build_tree,DNAbin-method build_tree,DNAStringSet build_tree,DNAStringSet-method |
| convert dataframe contained hierarchical relationship or other classes to treedata class | convert_to_treedata |
| (Data) Small subset of the HMP 16S dataset | data-hmp_aerobiosis_small hmp_aerobiosis_small |
| (Data) Genomic analysis identifies association of Fusobacterium with colorectal carcinoma (2012) | data-kostic2012crc kostic2012crc |
| (Data) simulated dataset. | data-test_otu_data test_otu_data |
| Differential expression analysis | diff_analysis diff_analysis.data.frame diff_analysis.phyloseq |
| diffAnalysisClass class | diffAnalysisClass-class |
| Extracting the internal tbl_df attribute of tibble. | dr_extract |
| Dropping Species with Few abundance and Few Occurrences | drop_taxa drop_taxa,data.frame drop_taxa,data.frame-method drop_taxa,phyloseq drop_taxa,phyloseq-method |
| extract the binary offspring of the specified internal nodes | extract_binary_offspring |
| generalized fold change | generalizedFC generalizedFC.default generalizedFC.formula |
| alpha index | get_alphaindex get_alphaindex,data.frame get_alphaindex,data.frame-method get_alphaindex,integer get_alphaindex,integer-method get_alphaindex,matrix get_alphaindex,matrix-method get_alphaindex,numeric get_alphaindex,numeric-method get_alphaindex,phyloseq get_alphaindex,phyloseq-method |
| Hierarchical cluster analysis for the samples | get_clust get_clust.data.frame get_clust.dist get_clust.phyloseq |
| get ordination coordinates. | get_coord get_coord.pcoa get_coord.prcomp |
| calculate the count or relative abundance of replicate element with a speficify column | get_count get_ratio |
| calculate distance | get_dist get_dist.data.frame get_dist.phyloseq |
| get the mean and median of specific feature. | get_mean_median |
| calculating related phylogenetic alpha metric | get_NRI_NTI get_NRI_NTI,data.frame get_NRI_NTI,data.frame-method get_NRI_NTI,matrix get_NRI_NTI,matrix-method get_NRI_NTI,phyloseq get_NRI_NTI,phyloseq-method |
| Performs a principal components analysis | get_pca get_pca.data.frame get_pca.phyloseq |
| performs principal coordinate analysis (PCoA) | get_pcoa get_pcoa.data.frame get_pcoa.dist get_pcoa.phyloseq |
| Methods for computation of the p-value | get_pvalue get_pvalue.glm get_pvalue.htest get_pvalue.lm get_pvalue.lme get_pvalue.negbin get_pvalue.QuadTypeIndependenceTest get_pvalue.ScalarIndependenceTest |
| obtain the result of rare curve | get_rarecurve get_rarecurve,data.frame get_rarecurve,data.frame-method get_rarecurve,phyloseq get_rarecurve,phyloseq-method |
| Generate random data list from a original data. | get_sampledflist |
| get the data of specified taxonomy | get_taxadf get_taxadf,data.frame get_taxadf,data.frame-method get_taxadf,phyloseq get_taxadf,phyloseq-method |
| generate the dataset for upset of UpSetR | get_upset get_upset,data.frame get_upset,data.frame-method get_upset,phyloseq get_upset,phyloseq-method |
| get the contribution of variables | get_varct get_varct.pcasample get_varct.pcoa get_varct.prcomp |
| generate a vennlist for VennDiagram | get_vennlist get_vennlist,data.frame-method get_vennlist,data.framet get_vennlist,phyloseq get_vennlist,phyloseq-method |
| taxonomy barplot | ggbartax ggbartax.data.frame ggbartax.phyloseq ggbartaxa |
| A box or violin plot with significance test | ggbox ggbox,alphasample ggbox,alphasample-method ggbox,data.frame ggbox,data.frame-method |
| plot the result of hierarchical cluster analysis for the samples | ggclust ggclust.treedata |
| boxplot for the result of diff_analysis | ggdiffbox ggdiffbox,diffAnalysisClass ggdiffbox,diffAnalysisClass-method |
| plot the clade tree with highlight | ggdiffclade ggdiffclade.data.frame ggdiffclade.diffAnalysisClass |
| significantly discriminative feature barplot | ggdiffbartaxa ggdifftaxbar ggdifftaxbar,diffAnalysisClass ggdifftaxbar,diffAnalysisClass-method ggdifftaxbar.featureMeanMedian |
| visualization of effect size by the Linear Discriminant Analysis or randomForest | ggeffectsize ggeffectsize.data.frame ggeffectsize.diffAnalysisClass |
| ordination plotter based on ggplot2. | ggordpoint ggordpoint.default ggordpoint.pcasample |
| Rarefaction alpha index | ggrarecurve ggrarecurve.data.frame ggrarecurve.phyloseq ggrarecurve.rarecurve |
| Import function to load the feature table and taxonomy table of dada2 | ImportDada2 import_dada2 mp_import_dada2 |
| Import function to load the output of qiime2. | ImportQiime2 import_qiime2 mp_import_qiime2 |
| (Data) An example data | mouse.time.mpse |
| Permutational Multivariate Analysis of Variance Using Distance Matrices for MPSE or tbl_mpse object | mp_adonis mp_adonis,grouped_df_mpse mp_adonis,grouped_df_mpse-method mp_adonis,MPSE mp_adonis,MPSE-method mp_adonis,tbl_mpse mp_adonis,tbl_mpse-method |
| aggregate the assays with the specific group of sample and fun. | mp_aggregate mp_aggregate,MPSE mp_aggregate,MPSE-method |
| calculate the mean/median (relative) abundance of internal nodes according to their children tips. | mp_aggregate_clade mp_aggregate_clade,grouped_df_mpse mp_aggregate_clade,grouped_df_mpse-method mp_aggregate_clade,MPSE mp_aggregate_clade,MPSE-method mp_aggregate_clade,tbl_mpse mp_aggregate_clade,tbl_mpse-method |
| Analysis of Similarities (ANOSIM) with MPSE or tbl_mpse object | mp_anosim mp_anosim,grouped_df_mpse mp_anosim,grouped_df_mpse-method mp_anosim,MPSE mp_anosim,MPSE-method mp_anosim,tbl_mpse mp_anosim,tbl_mpse-method |
| Calculating the balance score of internal nodes (clade) according to the geometric.mean/mean/median abundance of their binary children tips. | mp_balance_clade mp_balance_clade,grouped_df_mpse mp_balance_clade,grouped_df_mpse-method mp_balance_clade,MPSE mp_balance_clade,MPSE-method mp_balance_clade,tbl_mpse mp_balance_clade,tbl_mpse-method |
| Calculate the (relative) abundance of each taxonomy class for each sample or group. | mp_cal_abundance mp_cal_abundance,grouped_df_mpse mp_cal_abundance,grouped_df_mpse-method mp_cal_abundance,MPSE mp_cal_abundance,MPSE-method mp_cal_abundance,tbl_mpse mp_cal_abundance,tbl_mpse-method |
| calculate the alpha index with MPSE or tbl_mpse | mp_cal_alpha mp_cal_alpha,grouped_df_mpse mp_cal_alpha,grouped_df_mpse-method mp_cal_alpha,MPSE mp_cal_alpha,MPSE-method mp_cal_alpha,tbl_mpse mp_cal_alpha,tbl_mpse-method |
| [Partial] [Constrained] Correspondence Analysis with MPSE or tbl_mpse object | mp_cal_cca mp_cal_cca,grouped_df_mpse mp_cal_cca,grouped_df_mpse-method mp_cal_cca,MPSE mp_cal_cca,MPSE-method mp_cal_cca,tbl_mpse mp_cal_cca,tbl_mpse-method |
| Hierarchical cluster analysis for the samples with MPSE or tbl_mpse object | mp_cal_clust mp_cal_clust,grouped_df_mpse mp_cal_clust,grouped_df_mpse-method mp_cal_clust,MPSE mp_cal_clust,MPSE-method mp_cal_clust,tbl_mpse mp_cal_clust,tbl_mpse-method |
| Detrended Correspondence Analysis with MPSE or tbl_mpse object | mp_cal_dca mp_cal_dca,grouped_df_mpse mp_cal_dca,grouped_df_mpse-method mp_cal_dca,MPSE mp_cal_dca,MPSE-method mp_cal_dca,tbl_mpse mp_cal_dca,tbl_mpse-method |
| Calculate the distances between the samples or features with specified abundance. | mp_cal_dist mp_cal_dist,grouped_df_mpse mp_cal_dist,grouped_df_mpse-method mp_cal_dist,MPSE mp_cal_dist,MPSE-method mp_cal_dist,tbl_mpse mp_cal_dist,tbl_mpse-method |
| calculate the divergence with MPSE or tbl_mpse | mp_cal_divergence mp_cal_divergence,grouped_df_mpse mp_cal_divergence,grouped_df_mpse-method mp_cal_divergence,MPSE mp_cal_divergence,MPSE-method mp_cal_divergence,tbl_mpse mp_cal_divergence,tbl_mpse-method |
| Nonmetric Multidimensional Scaling Analysis with MPSE or tbl_mpse object | mp_cal_nmds mp_cal_nmds,grouped_df_mpse mp_cal_nmds,grouped_df_mpse-method mp_cal_nmds,MPSE mp_cal_nmds,MPSE-method mp_cal_nmds,tbl_mpse mp_cal_nmds,tbl_mpse-method |
| Principal Components Analysis with MPSE or tbl_mpse object | mp_cal_pca mp_cal_pca,grouped_df_mpse mp_cal_pca,grouped_df_mpse-method mp_cal_pca,MPSE mp_cal_pca,MPSE-method mp_cal_pca,tbl_mpse mp_cal_pca,tbl_mpse-method |
| Principal Coordinate Analysis with MPSE or tbl_mpse object | mp_cal_pcoa mp_cal_pcoa,grouped_df_mpse mp_cal_pcoa,grouped_df_mpse-method mp_cal_pcoa,MPSE mp_cal_pcoa,MPSE-method mp_cal_pcoa,tbl_mpse mp_cal_pcoa,tbl_mpse-method |
| Calculating related phylogenetic alpha metric with MPSE or tbl_mpse object | mp_cal_pd_metric mp_cal_pd_metric,grouped_df_mpse mp_cal_pd_metric,grouped_df_mpse-method mp_cal_pd_metric,MPSE mp_cal_pd_metric,MPSE-method mp_cal_pd_metric,tbl_mpse mp_cal_pd_metric,tbl_mpse-method |
| Calculating the different alpha diversities index with different depth | mp_cal_rarecurve mp_cal_rarecurve,grouped_df_mpse mp_cal_rarecurve,grouped_df_mpse-method mp_cal_rarecurve,MPSE mp_cal_rarecurve,MPSE-method mp_cal_rarecurve,tbl_mpse mp_cal_rarecurve,tbl_mpse-method |
| [Partial] [Constrained] Redundancy Analysis with MPSE or tbl_mpse object | mp_cal_rda mp_cal_rda,grouped_df_mpse mp_cal_rda,grouped_df_mpse-method mp_cal_rda,MPSE mp_cal_rda,MPSE-method mp_cal_rda,tbl_mpse mp_cal_rda,tbl_mpse-method |
| Calculating the samples or groups for each OTU, the result can be visualized by 'ggupset' | mp_cal_upset mp_cal_upset,grouped_df_mpse mp_cal_upset,grouped_df_mpse-method mp_cal_upset,MPSE mp_cal_upset,MPSE-method mp_cal_upset,tbl_mpse mp_cal_upset,tbl_mpse-method |
| Calculating the OTU for each sample or group, the result can be visualized by 'ggVennDiagram' | mp_cal_venn mp_cal_venn,grouped_df_mpse mp_cal_venn,grouped_df_mpse-method mp_cal_venn,MPSE mp_cal_venn,MPSE-method mp_cal_venn,tbl_mpse mp_cal_venn,tbl_mpse-method |
| This Function Provideds Several Standardization Methods for Community Data | mp_decostand mp_decostand,data.frame mp_decostand,data.frame-method mp_decostand,grouped_df_mpse mp_decostand,grouped_df_mpse-method mp_decostand,MPSE mp_decostand,MPSE-method mp_decostand,tbl_mpse mp_decostand,tbl_mpse-method |
| Differential expression analysis for MPSE or tbl_mpse object | mp_diff_analysis mp_diff_analysis,grouped_df_mpse mp_diff_analysis,grouped_df_mpse-method mp_diff_analysis,MPSE mp_diff_analysis,MPSE-method mp_diff_analysis,tbl_mpse mp_diff_analysis,tbl_mpse-method |
| Differential internal and tip nodes (clades) analysis for MPSE or tbl_mpse object | mp_diff_clade mp_diff_clade,grouped_df_mpse mp_diff_clade,grouped_df_mpse-method mp_diff_clade,MPSE mp_diff_clade,MPSE-method mp_diff_clade,tbl_mpse mp_diff_clade,tbl_mpse-method |
| Fit Dirichlet-Multinomial models to MPSE or tbl_mpse | mp_dmn mp_dmn,grouped_df_mpse mp_dmn,grouped_df_mpse-method mp_dmn,MPSE mp_dmn,MPSE-method mp_dmn,tbl_mpse mp_dmn,tbl_mpse-method |
| Dirichlet-Multinomial generative classifiers to MPSE or tbl_mpse | mp_dmngroup mp_dmngroup,grouped_df_mpse mp_dmngroup,grouped_df_mpse-method mp_dmngroup,MPSE mp_dmngroup,MPSE-method mp_dmngroup,tbl_mpse mp_dmngroup,tbl_mpse-method |
| Fits an Environmental Vector or Factor onto an Ordination With MPSE or tbl_mpse Object | mp_envfit mp_envfit,grouped_df_mpse mp_envfit,grouped_df_mpse-method mp_envfit,MPSE mp_envfit,MPSE-method mp_envfit,tbl_mpse mp_envfit,tbl_mpse-method |
| Extracting the abundance metric from MPSE or tbl_mpse object | mp_extract_abundance mp_extract_abundance,grouped_df_mpse mp_extract_abundance,grouped_df_mpse-method mp_extract_abundance,MPSE mp_extract_abundance,MPSE-method mp_extract_abundance,tbl_mpse mp_extract_abundance,tbl_mpse-method |
| extract the abundance matrix from MPSE object or tbl_mpse object | mp_extract_assays mp_extract_assays,grouped_df_mpse mp_extract_assays,grouped_df_mpse-method mp_extract_assays,MPSE mp_extract_assays,MPSE-method mp_extract_assays,tbl_mpse mp_extract_assays,tbl_mpse-method |
| extract the dist object from MPSE or tbl_mpse object | mp_extract_dist mp_extract_dist,grouped_df_mpse mp_extract_dist,grouped_df_mpse-method mp_extract_dist,MPSE mp_extract_dist,MPSE-method mp_extract_dist,tbl_mpse mp_extract_dist,tbl_mpse-method |
| extract the feature (OTU) information in MPSE object | mp_extract_feature mp_extract_feature,grouped_df_mpse mp_extract_feature,grouped_df_mpse-method mp_extract_feature,MPSE mp_extract_feature,MPSE-method mp_extract_feature,tbl_mpse mp_extract_feature,tbl_mpse-method |
| Extracting the PCA, PCoA, etc results from MPSE or tbl_mpse object | mp_extract_internal_attr mp_extract_internal_attr,grouped_df_mpse mp_extract_internal_attr,grouped_df_mpse-method mp_extract_internal_attr,MPSE mp_extract_internal_attr,MPSE-method mp_extract_internal_attr,tbl_mpse mp_extract_internal_attr,tbl_mpse-method |
| Extract the result of mp_cal_rarecurve with action="add" from MPSE or tbl_mpse object | mp_extract_rarecurve mp_extract_rarecurve,grouped_df_mpse mp_extract_rarecurve,grouped_df_mpse-method mp_extract_rarecurve,MPSE mp_extract_rarecurve,MPSE-method mp_extract_rarecurve,tbl_mpse mp_extract_rarecurve,tbl_mpse-method |
| Extract the representative sequences from MPSE object | mp_extract_refseq mp_extract_refseq,grouped_df_mpse mp_extract_refseq,grouped_df_mpse-method mp_extract_refseq,MPSE mp_extract_refseq,MPSE-method mp_extract_refseq,tbl_mpse mp_extract_refseq,tbl_mpse-method |
| extract the sample information in MPSE object | mp_extract_sample mp_extract_sample,grouped_df_mpse mp_extract_sample,grouped_df_mpse-method mp_extract_sample,MPSE mp_extract_sample,MPSE-method mp_extract_sample,tbl_mpse mp_extract_sample,tbl_mpse-method |
| extract the taxonomy tree in MPSE object | mp_extract_otutree mp_extract_taxatree mp_extract_tree mp_extract_tree,grouped_df_mpse mp_extract_tree,grouped_df_mpse-method mp_extract_tree,MPSE mp_extract_tree,MPSE-method mp_extract_tree,tbl_mpse mp_extract_tree,tbl_mpse-method |
| Filter OTU (Features) By Abundance Level | mp_filter_taxa mp_filter_taxa,grouped_df_mpse mp_filter_taxa,grouped_df_mpse-method mp_filter_taxa,MPSE mp_filter_taxa,MPSE-method mp_filter_taxa,tbl_mpse mp_filter_taxa,tbl_mpse-method |
| mp_fortify | mp_fortify |
| building MPSE object from biom-format file. | mp_import_biom |
| Import function to load the output of human_regroup_table in HUMAnN. | mp_import_humann_regroup |
| Import function to load the output of MetaPhlAn. | mp_import_metaphlan |
| Import function to load the output of qiime. | mp_import_qiime |
| Mantel and Partial Mantel Tests for MPSE or tbl_mpse Object | mp_mantel mp_mantel,grouped_df_mpse mp_mantel,grouped_df_mpse-method mp_mantel,MPSE mp_mantel,MPSE-method mp_mantel,tbl_mpse mp_mantel,tbl_mpse-method |
| Analysis of Multi Response Permutation Procedure (MRPP) with MPSE or tbl_mpse object | mp_mrpp mp_mrpp,grouped_df_mpse mp_mrpp,grouped_df_mpse-method mp_mrpp,MPSE mp_mrpp,MPSE-method mp_mrpp,tbl_mpse mp_mrpp,tbl_mpse-method |
| plotting the abundance of taxa via specified taxonomy class | mp_plot_abundance mp_plot_abundance,grouped_df_mpse mp_plot_abundance,grouped_df_mpse-method mp_plot_abundance,MPSE mp_plot_abundance,MPSE-method mp_plot_abundance,tbl_mpse mp_plot_abundance,tbl_mpse-method |
| Plotting the alpha diversity between samples or groups. | mp_plot_alpha mp_plot_alpha,grouped_df_mpse mp_plot_alpha,grouped_df_mpse-method mp_plot_alpha,MPSE mp_plot_alpha,MPSE-method mp_plot_alpha,tbl_mpse mp_plot_alpha,tbl_mpse-method |
| displaying the differential result contained abundance and LDA with boxplot (abundance) and error bar (LDA). | mp_plot_diff_boxplot mp_plot_diff_boxplot,grouped_df_mpse mp_plot_diff_boxplot,grouped_df_mpse-method mp_plot_diff_boxplot,MPSE mp_plot_diff_boxplot,MPSE-method mp_plot_diff_boxplot,tbl_mpse mp_plot_diff_boxplot,tbl_mpse-method |
| Visualizing the result of mp_diff_analysis with cladogram. | mp_plot_diff_cladogram |
| displaying the differential result contained abundance and LDA with manhattan plot. | mp_plot_diff_manhattan mp_plot_diff_manhattan,grouped_df_mpse mp_plot_diff_manhattan,grouped_df_mpse-method mp_plot_diff_manhattan,MPSE mp_plot_diff_manhattan,MPSE-method mp_plot_diff_manhattan,tbl_mpse mp_plot_diff_manhattan,tbl_mpse-method |
| The visualization of result of mp_diff_analysis | mp_plot_diff_res mp_plot_diff_res,grouped_df_mpse mp_plot_diff_res,grouped_df_mpse-method mp_plot_diff_res,MPSE mp_plot_diff_res,MPSE-method mp_plot_diff_res,tbl_mpse mp_plot_diff_res,tbl_mpse-method |
| Plotting the distance between the samples with heatmap or boxplot. | mp_plot_dist mp_plot_dist,grouped_df_mpse mp_plot_dist,grouped_df_mpse-method mp_plot_dist,MPSE mp_plot_dist,MPSE-method mp_plot_dist,tbl_mpse mp_plot_dist,tbl_mpse-method |
| Plotting the result of PCA, PCoA, CCA, RDA, NDMS or DCA | mp_plot_ord mp_plot_ord,grouped_df_mpse mp_plot_ord,grouped_df_mpse-method mp_plot_ord,MPSE mp_plot_ord,MPSE-method mp_plot_ord,tbl_mpse mp_plot_ord,tbl_mpse-method |
| Rarefaction alpha index with MPSE | mp_plot_rarecurve mp_plot_rarecurve,grouped_df_mpse-method mp_plot_rarecurve,grouped_tbl_mpse mp_plot_rarecurve,MPSE mp_plot_rarecurve,MPSE-method mp_plot_rarecurve,tbl_mpse mp_plot_rarecurve,tbl_mpse-method |
| Plotting the different number of OTU between group via UpSet plot | mp_plot_upset mp_plot_upset,grouped_df_mpse mp_plot_upset,grouped_df_mpse-method mp_plot_upset,MPSE mp_plot_upset,MPSE-method mp_plot_upset,tbl_mpse mp_plot_upset,tbl_mpse-method |
| Plotting the different number of OTU between groups with Venn Diagram. | mp_plot_venn mp_plot_venn,grouped_df_mpse mp_plot_venn,grouped_df_mpse-method mp_plot_venn,MPSE mp_plot_venn,MPSE-method mp_plot_venn,tbl_mpse mp_plot_venn,tbl_mpse-method |
| mp_rrarefy method | mp_rrarefy mp_rrarefy,grouped_df_mpse mp_rrarefy,grouped_df_mpse-method mp_rrarefy,MPSE mp_rrarefy,MPSE-method mp_rrarefy,tbl_mpse mp_rrarefy,tbl_mpse-method |
| select specific taxa level as rownames of MPSE | mp_select_as_tip mp_select_as_tip,grouped_df_mpse mp_select_as_tip,grouped_df_mpse-method mp_select_as_tip,MPSE mp_select_as_tip,MPSE-method mp_select_as_tip,tbl_mpse mp_select_as_tip,tbl_mpse-method |
| Count the number and total number taxa for each sample at different taxonomy levels | mp_stat_taxa mp_stat_taxa,grouped_df_mpse mp_stat_taxa,grouped_df_mpse-method mp_stat_taxa,MPSE mp_stat_taxa,MPSE-method mp_stat_taxa,tbl_mpse mp_stat_taxa,tbl_mpse-method |
| Construct a MPSE object | MPSE |
| MPSE accessors | colData<-,MPSE,DataFrame-method colData<-,MPSE,NULL-method MPSE-accessors otutree otutree,group_df_mpse otutree,MPSE otutree,MPSE-method otutree,tbl_mpse otutree,tbl_mpse-method otutree<- otutree<-,grouped_df_mpse otutree<-,grouped_df_mpse,NULL-method otutree<-,grouped_df_mpse,treedata-method otutree<-,MPSE otutree<-,MPSE,NULL-method otutree<-,MPSE,phylo-method otutree<-,MPSE,treedata-method otutree<-,tbl_mpse otutree<-,tbl_mpse,NULL-method otutree<-,tbl_mpse,treedata-method refsequence refsequence,MPSE refsequence,MPSE-method refsequence<- refsequence<-,MPSE refsequence<-,MPSE,NULL-method refsequence<-,MPSE,XStringSet-method rownames<-,MPSE rownames<-,MPSE-method taxatree taxatree,grouped_df_mpse taxatree,grouped_df_mpse-method taxatree,MPSE taxatree,MPSE-method taxatree,tbl_mpse taxatree,tbl_mpse-method taxatree<- taxatree<-,grouped_df_mpse taxatree<-,grouped_df_mpse,NULL-method taxatree<-,grouped_df_mpse,treedata-method taxatree<-,MPSE taxatree<-,MPSE,NULL-method taxatree<-,MPSE,treedata-method taxatree<-,tbl_mpse taxatree<-,tbl_mpse,NULL-method taxatree<-,tbl_mpse,treedata-method taxonomy<- taxonomy<-,MPSE taxonomy<-,MPSE,data.frame-method taxonomy<-,MPSE,matrix-method taxonomy<-,MPSE,NULL-method taxonomy<-,MPSE,taxonomyTable-method tax_table tax_table,grouped_df_mpse tax_table,grouped_df_mpse-method tax_table,MPSE tax_table,MPSE-method tax_table,tbl_mpse tax_table,tbl_mpse-method [,MPSE,ANY,ANY,ANY-method |
| MPSE class | MPSE-class |
| a container for performing two or more sample test. | multi_compare |
| ordplotClass class | ordplotClass-class |
| pcasample class | pcasample-class |
| print some objects | print print.grouped_df_mpse print.MPSE print.rarecurve print.tbl_mpse |
| read the qza file, output of qiime2. | read_qza |
| Create the scale of mp_plot_diff_cladogram. | scale_fill_diff_cladogram |
| set the color scale of plot generated by mp_plot_diff_boxplot | set_diff_boxplot_color |
| adjust the color of heatmap of mp_plot_dist | set_scale_theme |
| method extensions to show for diffAnalysisClass or alphasample objects. | show,alphasample-method show,diffAnalysisClass-method show,MPSE-method |
| Split Large Vector or DataFrame | split_data |
| split a dataframe contained one column | split_str_to_list |
| extract the taxonomy annotation in MPSE object | mp_extract_taxonomy mp_extract_taxonomy,grouped_df_mpse mp_extract_taxonomy,grouped_df_mpse-method mp_extract_taxonomy,MPSE mp_extract_taxonomy,MPSE-method mp_extract_taxonomy,tbl_mpse mp_extract_taxonomy,tbl_mpse-method taxonomy taxonomy,grouped_df_mpse taxonomy,grouped_df_mpse-method taxonomy,MPSE taxonomy,MPSE-method taxonomy,tbl_mpse taxonomy,tbl_mpse-method |
| theme_taxbar | theme_taxbar |
