- Fix: tax_fix no longer allows min_length of 0, as empty strings are (and were) always replaced
- Fix/Feat: comp_barplot, ord_explore, and tax_sort checks/warnings about unavailable counts can be disabled with counts_warn = FALSE
- Fix: no more cowplot legend extraction warnings in
ord_explore
- Fix: allow hex code colours in
ord_plot
- Fix:
comp_heatmaphelpersampleAnnotationwill now work with R 4.4
- corncob (a suggested dependency) back on CRAN - so no longer installed from GitHub
ibdphyloseq dataset added to microViz, as no longer included in corncob.
- Breaking change: va-wunifrac distance calculation is no longer available, as it is not available in GUniFrac 1.8
- Note: If needed,
corncobcan now only be installed from GitHub, as is currently not available from CRAN.corncobis a suggested dependency of microViz from which data is borrowed for use in several examples, and which is needed is bbdml models are requested in tax_model.
taxatree_modelsnow accepts transformation arguments to allow transformation after aggregation at each rank
- Fix:
taxatree_stats_p_adjustcan accept multiple grouping variables without specifying new_var.
- Fix:
comp_barplottaxon ordering is now correct when tax_level is set to "Taxon"
- Fix: Small internal fix to avoid renderggiraph deprecation warning in ord_explore.
- Fix: Internal fix to report NAs in OTU table more gracefully. (ps_counts issue #109)
- Fix:
tax_select()tax_list argument can now actually take a list (Issue #100)
- Fix: small internal fix for compatibility with next R version (relating to loss of stringsAsFactors global option)
- Fix for dplyr version 1.1.0 warnings e.g. about across() wanting explicit .cols use
- Fix shao19 example data: family rank in tax table now correctly shows families
- Bug fix: manual direct labelling of
taxatree_plotswithtaxatree_labelsandtaxatree_plot_labelsworks properly also with phyloseq object that lack a rooting rank (e.g. kingdom) - Bug fix:
comp_barplotbars are now in the correct order again when using tax_level = "unique" - New Getting Started article
- Bug fix: manual direct labelling of
taxatree_plotswithtaxatree_labelsandtaxatree_plot_labelsworks properly (without losing stats info for any rank)
taxatree_plotkeyIMPORTANT BUG FIX: layout now matches taxatree_plots again- Fixed broken ReadMe links
ps_getcan return phyloseq with taxon counts when counts = TRUE and counts are available
taxatree_plotsand keys more robust #43 and no deprecation warnings #80tax_transformadd argument accepts "halfmin" again #77tax_topcan use_counts #78- Compatibility with old R versions 3.6.* improved (explicit stringsAsFactors = FALSE)
- Updates for compatibility with ggplot2 3.4.0
- Move DT, ggraph and tidygraph to suggested dependencies
Major internal changes from S3 ps_extra to S4 psExtra objects. See article about this change
This version also introduces changes around tax_model and taxatree_models functionality.
- Using the
$operator to access parts of the old "ps_extra" S3 class will no longer work and must be replaced with accessor functions, e.g.ps_get - "ps_extra" objects generated with older versions will not be compatible with version 0.10.0 and can be converted to the new "psExtra" S4 objects with
upgrade_ps_extra_to_psExtra tax_modelandtaxatree_modelparallel processing with future and future.apply is off by default, and needs to be enabled with argument use_future = TRUE.tax_modelattaches results to psExtra object by default, but you can restore old behaviour with return_psx = FALSEcomp_barplot"other" taxa category renamed to "Other" by default
tax_modelandtaxatree_modelcan now run multiple models per taxon, by accepting lists for formula or variables arguments. This allows running e.g. three simple regression models per taxon with predictors a, b, and c with variables = list("a", "b", "c")cor_testis a new simple wrapper aroundstats::cor.testwith a y~x formula interface, allowing its use intax_model
- No more deprecation warnings in
taxatree_plot_labels
comp_barplotgains x argument, to change default x aesthetic to something other than SAMPLE, which is useful for (faceted) plotting of repeated samples from the same site/individual over time or in different conditions when some samples are missing (see compositions tutorial article)ps_seriatecan now aggregate taxa before seriation (returns unaggregated still)
- Custom reordering of taxa on
comp_barplotis now easier, just name the taxa you want to see first in the tax_order argument, and they will be brought to the front tax_reorderis exported, and now accepts a subset of all available taxa names (powering the improvement in comp_barplot)
- Bump rlang dependency version to 1.0.0 fixing #69
tax_renameaccepts integerish values for pad_digits argument
otu_getcorrectly subsets samples or taxa if requested- heatmaps with one row or column can be plotted without explicitly suppressing seriation
Robust clr and robust aitchison distance are now supported following their inclusion in vegan - tax_transform supports "rclr" (robust centered log ratio) - dist_calc supports "robust.aitchison" distance (as rclr & euclidean distance)
-
ps_dedupenow allows keeping a specified number of samples per group, not just one, which could be useful for e.g. keeping the first 2 samples per participant or site. -
shao19 dataset now included in microViz for use in the "Learn microbiome analysis with microViz" tutorial
ps_dedupenow deduplicates samples correctly when duplicates are specified with multiple variables, and provides a labelling-only mode to check duplicate identification result before removal.
- New function
tax_paletteallows easy creation of a fixed colour palette for taxa, to use with e.g. comp_barplot - New convenience functions
ps_calc_diversityandps_calc_richnessto calculate a diversity or richness index (using microbiome package functions) and add to phyloseq sample data - New function
tax_renameallows renaming of taxa using unique combination of classification at any chosen rank and abundance of that taxon (e.g. ASV145 becomes Bifidobacterium-002, which can be interpreted as the second most abundant Bifidobacterium ASV) tax_sortcan now sort taxa "asis" (i.e. do nothing), which now permits upfront custom sorting of taxa for use incomp_barplottax_sortcan now transform taxa temporarily for sorting e.g. to sort by mean compositional (%) relative abundance
comp_heatmap and cor_heatmap and their helpers are largely rewritten. For guidance, see the new website article on heatmaps.
taxAnnotationandvarAnnotationannotation helper functions replace the deprecatedtax_annoandvar_annofunctionssampleAnnotationis added for coordinating sample annotations oncomp_heatmap- various
anno_*helpers for each of the annotation coordinating functions above
taxatree_plotscan now show symbols indicating multiple levels of statistical significancetaxatree_plots: it is now easier to use other colour palettes with their default luminance
ord_explorecan perform "binary" transformations, unlocking interactive use of Binary Jaccard etc.tax_transformgainsaddargument to simply add a constant value to all otu_table values before transformation (as an alternative tozero_replace)tax_scalegainskeep_countsargument for consistency withtax_transform
tax_modelnow only requirescorncobto be installed when actually usedord_explorebarplot numerical inputs are now debounced to prevent lag from repeated redrawing
The taxatree_* family of functions are largely rewritten. For guidance, see the new website article on statistical modelling of taxa.
taxatree_modelsnow attaches resulting list to ps_extrataxatree_models2statsmust be run on the output oftaxatree_modelsbefore usingtaxatree_plotstaxatree_plotshas different arguments and can now be directly labelled withtaxatree_plot_labelswhentaxatree_labelis run first to identify which taxa to label.taxatree_plotkeyhas different arguments, with more flexible labelling conditions and a smarter label positioning approach.tax_modelandtaxatree_modelsnow use "lm" type by default, instead of "bbdml", ascorncobis only a suggested dependency.
ord_plotdefault labels now havealpha= 1 for both taxa and constraints (previously 0.8)ord_plot"auto"matic loading/constraint vector length scalar adjustment improvement: now uses both axes
comp_barplotnow uses bray-curtis by default for sample ordering (instead of aitchison) as this generally looks bettercomp_barplotnow expects palette argument colours in first-to-last order, which is more intuitive than the previous reverse orderdistinct_palettenow adds "lightgrey" to end by default
tax_filter'sis_countsargument replaced byuse_counts, allowing it to filter ps_extra objects using stored count data (i.e. aftertax_transform).comp_heatmapcan no longer transform data internally, but accepts data already transformed withtax_transformand uses stored count data in the ps_extra for any taxa annotationstax_annoheatmap annotation default style slightly changed.tax_names2rankreplaces deprecatedtax_names2tt
ord_plotarrow labels can now be rotated with the help oftax_lab_style()andconstraint_lab_style()ps_calc_dominantfunction added, for conveniently identifying the dominant taxon in each phyloseq sampledistinct_palettegains "kelly" and "greenArmytage" palettes and helpfully adds "lightgrey" to the end by default for convenient use as the palette argument tocomp_barplottax_transformcan now chain multiple transformations together and records these transformations in the ps_extra outputtax_mutatefunction added, for modifying the tax_table rank variables withdplyrmutatesyntaxtax_sortcan now sort ps_extra objects- heatmap annotation helper
tax_annono longer requires 'column' or 'row' to be specified in advance prev, a low level helper function for calculating taxon prevalence now exported- Various phyloseq accessor functions now work with ps_extra objects e.g. taxa_names, sample_names
cor_heatmapandcomp_heatmapnow respect column seriation arguments when different to row seriationcomp_barplotnow actually orders grouped samples by similarity AFTER splitting into groups, as documented
Updated citation information for JOSS publication. No other changes.
Release accompanying JOSS manuscript acceptance.
- Includes a fix (hopefully temporary) for incorrect barplot legend in ord_explore caused by bug introduced by ggplot2 version 3.3.4 noted at tidyverse/ggplot2#4511
ord_plotgainsvec_*helper functions for generating lists for styling taxa and constraint vectors/arrows (vec_constraint,vec_tax_allandvec_tax_sel)
ord_exploreshapes selection bug fixed by limiting to 5 shapes returned by newscale_shape_girafe_filledfunction
stat_chullsadded, for drawing convex hulls on ord_plot and ord_explore ordinationsadd_pathsadded, for drawing geom_paths connecting a subset of samples (over time) on an ordination plot
phyloseq_validateno longer checks "unique" tax_table rank column for NAs or nchar<4 (avoiding warnings in ord_explore caused by short taxa_names)
ord_explorecan now draw stat_ellipse or taxa loading vectorstax_aggerror messages now include personalised suggested tax_fix code
ord_exploreShiny app GUI can now also be used to interactively generate ordination plots, and to generateord_plotcodeord_plotbug fix - can now plot any dimension- Removed deprecated
tax_fill_unknownsfunction
phyloseq_validateverbose = FALSE is actually silent now.
ord_explorenow compatible with Shiny version >=1.5.0tax_fixnow sends messages about fixing completely anonymous rows, instead of warnings
Allows ps_seriate, ps_arrange, ps_reorder, ps_mutate, and ps_select to work directly with ps_extra objects, as this can be helpful when quickly exploring / printing aggregated data, as in the new "Working with phyloseq objects" tutorial.
tax_fixreplaces the deprecatedtax_fill_unknowns,tax_fixhas all the same arguments except the 'levels' argument, which was removed
tax_fix_interactiveShiny app will help you clean up your taxonomy table withtax_fix
ord_plot_irisandord_exploreno longer take ps argument of untransformed counts, because (by default)tax_transformnow keeps the untransformed counts otu_table in the ps_extra object
ord_explorenow allows much better control over selection of points (usingggiraphfunctionality)ord_plotnow has interactive option withggiraphpackageord_plot_irisgains ord_plot argument, allowing a simple pairing of iris plot and ordination to be made more easilycomp_barplot(and by extensionord_plot_iris) can now be made interactive in a simple fashion, using ggiraph for hover/tooltip interaction with taxa
This is the first public release version of microViz. It is still under active development, so pay attention to the following:
- Minor version changes (e.g. 0.5.* to 0.6.0) will signal that breaking changes have been made, i.e. installing the new version may break some previously working code. Breaking changes will be listed in this document.
- Patch versions (e.g. 0.5.1 to 0.5.2) will be used to release new features and bug fixes, which should not break existing code. Please let me know if it does anyway!
tax_aggargument agg_level renamed to rank.tax_aggreturns taxa in different order than before (and now different order from, but same aggregation as,microbiome::aggregate_taxa()). tax_agg now checks if taxa cannot be uniquely identified at the specified rank level. (now also about twice as fast)tax_fill_unknownsx arg renamed to ps. Also now stops when unknown values are detected to the left of known values in the tax_table, as this should always be wrong/need fixing. Also, by default it now searches a larger list of probably unknown/uninformative tax_table values e.g. "k__NA", "p__Unknown" will now be replaced
comp_barplotgets merge_other argument, which, when FALSE, shows full diversity of samples by outlining individual taxa within the (grey) "other" category!tax_sortfor sorting taxa in tax_table and otu_table by several name or abundance options (deletes phy_tree if present!)tax_transformcan take a rank argument, to perform aggregation (internally using tax_agg) and transformation with one function, and record the results. This is now the recommended usage!tax_transformnew transformation = "binary" can convert to presence/absence data (used bytax_sortfor by = "prev")tax_topfor flexibly returning top n taxa, at chosen rank, with ordering bytax_sort
cor_heatmapandcomp_heatmapargument changed: 'taxa_which' replaced with 'taxa_side' for easier control over where taxa annotations are placed (default behaviour stays the same)
- Optionally annotate
cor_heatmapwith variable distributions usingvar_annoand its helpers:anno_var_boxandanno_var_hist cor_heatmapgets 'var_fun' argument for transforming variables before correlatingphyloseq_validatechecks for zero taxa, which can happen after filtering samplestax_filtergets undetected arg (greater than), as optional alternative to prev_detection_threshold (greater than or equal to)
- heatmaps should handle NAs better (
viz_heatmapinternal function fix) heat_palettecan set range arg manually now without errors
- minor versions from 0.5 will now get a memorable name, probably referring to features added since the last minor version
cor_heatmapfor microbe-metadata correlation heatmapscomp_heatmapfor visualising taxonomic composition across samples (ordered/clustered)ord_calccan now guess which method the user wants by default (by checking for presence of distance matrix and constraints)ord_plotauto_caption size can now be set, and it also now exposes thecoord_*args: expand and clipord_plot_irisnow handles multiple rings of anno_binary annotations, and anno_binary position is now closer when no anno_colour is setord_exploreshiny app menu styling is a little cleaner (but still needs some love)tax_scalefor applyingbase::scale()to phyloseq otu_tabletax_namefor easily setting informative unique phyloseq taxa_names
dist_permanova's obsolete return arg removedtax_filtergets explicit handling of compositional inputtax_fill_unknownsgets better handling of fully unclassified taxataxatree_nodesnow checks for cross-rank name duplications, which would mess up the taxatree graph structure
ord_explorenow works with ps_extra classestax_fill_unknownsgives informative error on data with only one taxonomic ranktax_filterps argument default removed
ord_calcnow correctly returns subsetted phyloseq in ps_extra obj after constrained ordinationtaxatree_plotsandtaxatree_plotkeynow have reactive automatic minimum node and edge sizes that depend on the set maxes
dist_permanovareplacespermanovafor naming consistency and guiding usercomp_barplotreplacesplot_comp_barin anticipation of (a) future heatmap function(s) named comp_heatmap or similar
New "ps_extra" class (S3) conveniently stores phyloseq object alongside any calculated distance matrix, ordination and permanova models, as well as records of tax_agg and tax_transform calls. "ps_extra" class objects have a pretty and compact print method, a simple list structure, and convenient accessor functions to return each component: ps_get, info_get, dist_get, ord_get, perm_get, bdisp_get.
- Taxon modelling updates:
tax_modelandtaxatree_modelscan handle linear modeling e.g. on compositional (TS-Scaled) datataxatree_plotshas more sensible defaults (automatic symmetrical colour limits and variable selection based on model type)
ord_plot_iristhedataarg is replaced withordand conditionally optionalpsarg for when data inordhave been transformedpermanovaalways uses adonis2 now, so that arg is removed, and replaced withbyargument to set sums of squares choice
ord_plotgets acenterargument to center expand the plot limits to center around zero (useful when pairing withord_plot_iris)ord_explorecan now also display ordinations that don't use distances like PCA and RDA (as well as PCoA of course)ord_exploregains apsarg (for untransformed version) and other tweaks to facilitate using transformed data inord
ord_plot_irisannotation args are now NULL by default.microbiome::aggregate_top_taxais copied directly intomicroVizto avoid its coming deprecation and the current warning.
taxatree_modelsandtaxatree_plotsbring tree-based visualisations of statistical models
tax_modelreplacestax_model_corncobas a function that will eventually be generalised to use other model typestaxatree_plotsandtaxatree_plotkeyreplaces the rudimentarytaxatree_plot
ord_exploreallows interactive exploration of the composition of ordinated samples usingShiny
ord_plot_irisfor pca-ordered circular compositional barplots to pair withord_plotoutputps_selectfor easily selecting variables within phyloseq sample dataord_plotexposes scaling argument
calc_dist-->dist_calcbeta_disper-->dist_bdispordin8-->ord_calcplot_ordin8-->ord_plotmodel_tax_corncob-->tax_model_corncob
plot_comp_bar- groups argument renamed to group_by for consistency with new facet_by argument
- drop_unused_vars replaced with keep_all_vars which defaults to TRUE
ps_seriatefor ordering phyloseq samples by similarity
ps_filterallows filtering ofphyloseqsamples by values of variables insample_data(wrapper arounddplyr'sfilterfunction)
ps_mutateno longer needs.acrossargument to usedplyr::across()
ps_dedupebug fix method = "readcount" now correctly keeps all samples that "first" or "last" methods do
ps_arrangeallows reordering ofphyloseqsamples by values of variables insample_dataorotu_table(wrapper arounddplyr'sarrangefunction)ps_otu2samdatadd taxon abundance variables fromphyloseqotu_tabletosample_datafor use in plotting etc
ps_mutateallowing easy and piped modification ofphyloseqsample_data(wrapper arounddplyr'smutatefunction)ps_joinallows easy and piped addition of a dataframe of data tophyloseqsample_data(wrapper arounddplyr's*_joinfunctions)
plot_ordin8arguments changed to allow easier sizing and styling of all vectors and labelsplot_ordin8default styling of taxon and constraint vectors and labels is changed: background vectors are now semi-transparent and dashed lines are not used any more by default (but can be set)
ordin8andplot_ordin8get basic support for CCA and NMDS methods finallyplot_comp_bargetsorder_samples_with_all_taxaandtax_transform_for_ordering- Documentation of manual sample ordering across
plot_comp_bargroups added to Visualising Compositions article on website. - Documentation of experimental polar coordinates and PCA_angle sorting added in new article called PCA-sorted polar composition plots, on website.
-
phyloseq_validatenow fixes otu_tables stored as integers and messages user about suspicious or NA tax_table entries and this happens as part ofplot_comp_barandplot_ordin8 -
plot_comp_barandplot_ordin8gaintaxon_renamerargument to allow you to customise the taxon names on these plots -
plot_comp_barcan now handle missing values in the grouping variable by converting NAs to "NA"s -
Some functions renamed for naming consistency:
prepend_ranks->tax_prepend_rankstax_model_corncob->model_tax_corncobcorncob_models_to_var_stats->modelsmodels2stats_corncobtax_tree_nodes/edges/plot->taxatree_...
- Added a
NEWS.mdfile to track changes to the package.