Package: comparpq 0.2.1

comparpq: Compare and Analyse Multiple 'phyloseq' Objects

Compare and analyse multiple 'phyloseq' objects from the 'R' 'phyloseq' package. Provides tools for taxonomic comparison, accuracy metrics computation (confusion matrix approach with FDR, TPR, F1 score, and MCC), and visualizations including bubble plots, Venn diagrams, and diversity estimation across groups of microbiome datasets.

Authors:Adrien Taudière [aut, cre, cph]

comparpq_0.2.1.tar.gz
comparpq_0.2.1.zip(r-4.7)comparpq_0.2.1.zip(r-4.6)comparpq_0.2.1.zip(r-4.5)
comparpq_0.2.1.tgz(r-4.6-any)comparpq_0.2.1.tgz(r-4.5-any)
comparpq_0.2.1.tar.gz(r-4.7-any)comparpq_0.2.1.tar.gz(r-4.6-any)
comparpq_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
comparpq/json (API)

# Install 'comparpq' in R:
install.packages('comparpq', repos = c('https://adrientaudiere.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adrientaudiere/comparpq/issues

Pkgdown/docs site:https://adrientaudiere.github.io

On CRAN:

Conda:

3.09 score 1 stars 19 scripts 58 exports 197 dependencies

Last updated from:c42519a888. Checks:8 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR742
source / vignettesERROR466
linux-release-x86_64ERROR695
macos-release-arm64ERROR546
macos-oldrel-arm64ERROR501
windows-develERROR747
windows-releaseERROR850
windows-oldrelERROR870
wasm-releaseOK276

Exports:add_external_seq_pqadd_phyloseqadd_shuffle_seq_pqadonis_lpqaldex_lpqancombc_lpqapply_to_lpqbubbles_pqcommunity_sharing_barplot_pqcommunity_sharing_pqcompare_refseqdefault_sharing_metricsdiv_pqestim_cor_lpqestim_cor_pqestim_diff_lpqestim_diff_pqfactor_formatterfilter_common_lpqfind_primers_pqformattable_lpqformattable_lpq_fullgg_aldex_plotgg_bubbles_pqgg_hill_lpqgg_maaslin3_plotglmulti_lpqlist_phyloseqmaaslin3_pqmake_sharing_metricmerge_lpqmidasim_pqmultipatt_lpqmultiply_counts_pqn_levels_lpqpermute_da_pqrainplot_taxo_narefseq_comp_lpqremove_phyloseqrename_ranks_pqresolve_taxo_conflictselect_ranks_pqshared_mod_lpqsimple_venn_pqtaxo2treetaxtab_replace_pattern_by_NAtc_bartc_circletc_congruence_metricstc_df_pqtc_heatmaptc_linked_treestc_metrics_mocktc_metrics_mock_vectc_points_matrixtc_sankeyupdate_list_phylosequpset_lpq

Dependencies:abindade4alphahullapeaplotaskpassbase64encBHBiobaseBiocGenericsBiocParallelbiomformatBiostringsbitopsbootbslibcachemcigarillocirclizecliclustercodetoolscollapsecolorspacecpp11crayoncubaturedada2data.tabledbmssDelayedArraydeldirdigestdiventdoFuturedplyrEntropyEstimationevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRformattablefsfutile.loggerfutile.optionsfuturefuture.applygdtoolsgenericsGenomicAlignmentsGenomicRangesggalluvialggfunggiraphggnewscaleggplot2ggplotifyggtreeGlobalOptionsglobalsgluegoftestGPArotationgridGraphicsgtablehighrhtmltoolshtmlwidgetshwriterigraphinterpIRangesisobanditeratorsjpegjquerylibjsonlitekmerknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelistenvlme4lmerTestmaaslin3magrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvMIDASimmimeminqamiraiMiscMetabarmnormtmultcompmultcompViewmulttestmvtnormnanonextnlmenloptrnumDerivopenssloptparseparallellypatchworkpermutephylogramphyloseqpillarpixmappkgconfigplyrpngpolyclippracmaprogressrpsychpurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreformulasreshape2RhtslibrlangrmarkdownRsamtoolsS4ArraysS4VectorsS7sandwichsassscalesscamSeqinfosgeostatshapeShortReadsnowspSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilssplancsstringistringrSummarizedExperimentsurvivalsyssystemfontstensorTH.datatibbletidyrtidyselecttidytreetinytextreeioutf8vctrsveganviridisLitewithrxfunXVectoryamlyulab.utilszoo

Readme and manuals

Help Manual

Help pageTopics
Subset a 'list_phyloseq' object[.list_phyloseq
Extract a single phyloseq object from a 'list_phyloseq'[[.list_phyloseq
Add external sequences to a phyloseq objectadd_external_seq_pq
Add a phyloseq object to a list_phyloseqadd_phyloseq
Add fake sequences by shuffling existing ones in a phyloseq objectadd_shuffle_seq_pq
PERMANOVA analysis on each phyloseq object in a list_phyloseqadonis_lpq
ALDEx2 analysis on each phyloseq object in a list_phyloseqaldex_lpq
ANCOM-BC analysis on each phyloseq object in a list_phyloseqancombc_lpq
Apply a function to all phyloseq objects in a list_phyloseqapply_to_lpq
Bubble plot of phyloseq object with observablehqbubbles_pq
Companion bar chart for 'community_sharing_pq()'community_sharing_barplot_pq
Community sharing plot: modalities as pie nodes with multi-metric linkscommunity_sharing_pq
Compare refseq slots between two phyloseq objectscompare_refseq
Default metrics for 'community_sharing_pq()'default_sharing_metrics
Diversity indices per sample, optionally grouped by a modalitydiv_pq
Estimation statistics for numeric correlation on a list_phyloseqestim_cor_lpq
Estimation statistics for numeric variable correlation on a phyloseq objectestim_cor_pq
Estimation statistics for categorical comparisons on a list_phyloseqestim_diff_lpq
Estimation statistics for categorical comparisons on a phyloseq objectestim_diff_pq
Format factor columns with funky colored backgroundsfactor_formatter
Filter phyloseq objects to keep only shared samples and/or taxafilter_common_lpq
Find taxa whose reference sequences match primer sequencesfind_primers_pq
Formattable visualization for list_phyloseq summaryformattable_lpq
Extended formattable for list_phyloseq with comparison infoformattable_lpq_full
ggplot2 version of ALDEx2 diagnostic plotsgg_aldex_plot
Circle-packed bubble plot of a phyloseq object using ggplot2gg_bubbles_pq
Scatter plots of Hill diversity across pairs of phyloseq objectsgg_hill_lpq
Plot MaAsLin3 resultsgg_maaslin3_plot
Automated model selection for Hill diversity on each phyloseq in a list_phyloseqglmulti_lpq
Number of phyloseq objects in a 'list_phyloseq'length.list_phyloseq
S7 class for comparing phyloseq objectslist_phyloseq
Run MaAsLin3 differential abundance analysis on a phyloseq objectmaaslin3_pq
Build a single metric definition for 'community_sharing_pq()'make_sharing_metric
Merge a list_phyloseq into a single phyloseq objectmerge_lpq
Simulate microbiome data with differential abundance using MIDASimmidasim_pq
Indicator species analysis on each phyloseq object in a list_phyloseqmultipatt_lpq
Multiply OTU counts conditionally based on sample metadatamultiply_counts_pq
Count unique taxonomic levels across phyloseq objectsn_levels_lpq
Names of phyloseq objects in a 'list_phyloseq'names.list_phyloseq
Simulate differential abundance by redistributing OTU countspermute_da_pq
Print a reference-sequence comparisonprint.compare_refseq
Print correlation estimation statistics for a list of phyloseq objectsprint.estim_cor_lpq_result
Print correlation estimation statistics for a phyloseq objectprint.estim_cor_pq_result
Print categorical estimation statistics for a list of phyloseq objectsprint.estim_diff_lpq_result
Print categorical estimation statistics for a phyloseq objectprint.estim_diff_pq_result
Print a 'list_phyloseq' objectprint.list_phyloseq
Print a reference-sequence similarity comparison across phyloseq objectsprint.refseq_comp_lpq_result
Rainplot of the nb taxa assigned (not NA)rainplot_taxo_na
Compare refseq sequences across all objects in a list_phyloseqrefseq_comp_lpq
Remove a phyloseq object from a list_phyloseqremove_phyloseq
Rename names of ranks in the tax_table slot of a phyloseq objectrename_ranks_pq
Resolve taxonomic conflict in the tax_table of a phyloseq objectresolve_taxo_conflict
Select taxonomic ranks in a phyloseq objectselect_ranks_pq
Display shared sample_data modalitiesshared_mod_lpq
Venn diagram of shared taxa across sample groupssimple_venn_pq
Convert taxonomy dataframe to phylogenetic treetaxo2tree
Replace taxonomic value with a given pattern by NAtaxtab_replace_pattern_by_NA
Barchart of ratio to compare 2 taxonomic rankstc_bar
Circle of correspondence between two taxonomic levelstc_circle
Compute congruence metrics between two taxonomic assignmentstc_congruence_metrics
Contingency table of two taxonomic rankstc_df_pq
Heatmap of correspondence between two taxonomic rankstc_heatmap
Plot two taxonomy trees with linked correspondencestc_linked_trees
Compute accuracy metrics of multiple taxonomic assignations method using mock for multi-rank and multi assignation methodstc_metrics_mock
Compute accuracy metrics of taxonomic assignation using a mock (known) community for one ranktc_metrics_mock_vec
Matrix of point to compare two taxonomic rankstc_points_matrix
Sankey diagram to compare two taxonomic rankstc_sankey
Update the summary table and comparison characteristicsupdate_list_phyloseq
UpSet or Venn plot of shared taxonomic values across phyloseq objectsupset_lpq