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Changelog

Source: NEWS.md

microViz 0.12.7

  • Fix: dist_permanova now works under R version 4.5.0

microViz 0.12.6

  • Fix: ord_plot score retrieval is now compatible with vegan 2.7.0

microViz 0.12.5

  • 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

microViz 0.12.4

  • Fix: no more cowplot legend extraction warnings in ord_explore

microViz 0.12.3

  • Fix: allow hex code colours in ord_plot

microViz 0.12.2

  • Fix: comp_heatmap helper sampleAnnotation will now work with R 4.4

microViz 0.12.1

  • corncob (a suggested dependency) back on CRAN - so no longer installed from GitHub
  • ibd phyloseq dataset added to microViz, as no longer included in corncob.

microViz 0.12.0

  • Breaking change: va-wunifrac distance calculation is no longer available, as it is not available in GUniFrac 1.8
  • Note: If needed, corncob can now only be installed from GitHub, as is currently not available from CRAN. corncob is 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.

microViz 0.11.0

  • taxatree_models now accepts transformation arguments to allow transformation after aggregation at each rank

microViz 0.10.11

  • Fix: taxatree_stats_p_adjust can accept multiple grouping variables without specifying new_var.

microViz 0.10.10

  • Fix: comp_barplot taxon ordering is now correct when tax_level is set to “Taxon”

microViz 0.10.9

  • 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)

microViz 0.10.8

  • Fix: small internal fix for compatibility with next R version (relating to loss of stringsAsFactors global option)

microViz 0.10.7

  • Fix for dplyr version 1.1.0 warnings e.g. about across() wanting explicit .cols use

microViz 0.10.6

  • Fix shao19 example data: family rank in tax table now correctly shows families

microViz 0.10.5

  • Bug fix: manual direct labelling of taxatree_plots with taxatree_labels and taxatree_plot_labels works properly also with phyloseq object that lack a rooting rank (e.g. kingdom)
  • Bug fix: comp_barplot bars are now in the correct order again when using tax_level = “unique”
  • New Getting Started article

microViz 0.10.4

  • Bug fix: manual direct labelling of taxatree_plots with taxatree_labels and taxatree_plot_labels works properly (without losing stats info for any rank)

microViz 0.10.3

  • taxatree_plotkey IMPORTANT BUG FIX: layout now matches taxatree_plots again
  • Fixed broken ReadMe links

microViz 0.10.2

Features

  • ps_get can return phyloseq with taxon counts when counts = TRUE and counts are available

Bug fixes

  • taxatree_plots and keys more robust #43 and no deprecation warnings #80
  • tax_transform add argument accepts “halfmin” again #77
  • tax_top can use_counts #78
  • Compatibility with old R versions 3.6.* improved (explicit stringsAsFactors = FALSE)

microViz 0.10.1

  • Updates for compatibility with ggplot2 3.4.0
  • Move DT, ggraph and tidygraph to suggested dependencies

microViz 0.10.0

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.

Breaking changes

  • 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_model and taxatree_model parallel processing with future and future.apply is off by default, and needs to be enabled with argument use_future = TRUE.
  • tax_model attaches results to psExtra object by default, but you can restore old behaviour with return_psx = FALSE
  • comp_barplot “other” taxa category renamed to “Other” by default

Features

  • tax_model and taxatree_model can 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_test is a new simple wrapper around stats::cor.test with a y~x formula interface, allowing its use in tax_model

Fixes

  • No more deprecation warnings in taxatree_plot_labels

microViz 0.9.7

Features

  • comp_barplot gains 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_seriate can now aggregate taxa before seriation (returns unaggregated still)

microViz 0.9.6

Features

  • Custom reordering of taxa on comp_barplot is 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_reorder is exported, and now accepts a subset of all available taxa names (powering the improvement in comp_barplot)

Fixes

microViz 0.9.5

Fixes

  • tax_rename accepts integerish values for pad_digits argument

microViz 0.9.4

Fixes

  • otu_get correctly subsets samples or taxa if requested
  • heatmaps with one row or column can be plotted without explicitly suppressing seriation

microViz 0.9.3

Features

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)

microViz 0.9.2

Features

  • ps_dedupe now 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

Fixes

  • ps_dedupe now deduplicates samples correctly when duplicates are specified with multiple variables, and provides a labelling-only mode to check duplicate identification result before removal.

microViz 0.9.1

Features

  • New function tax_palette allows easy creation of a fixed colour palette for taxa, to use with e.g. comp_barplot
  • New convenience functions ps_calc_diversity and ps_calc_richness to calculate a diversity or richness index (using microbiome package functions) and add to phyloseq sample data
  • New function tax_rename allows 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_sort can now sort taxa “asis” (i.e. do nothing), which now permits upfront custom sorting of taxa for use in comp_barplot
  • tax_sort can now transform taxa temporarily for sorting e.g. to sort by mean compositional (%) relative abundance

microViz 0.9.0

Heatmaps major changes

comp_heatmap and cor_heatmap and their helpers are largely rewritten. For guidance, see the new website article on heatmaps.

  • taxAnnotation and varAnnotation annotation helper functions replace the deprecated tax_anno and var_anno functions
  • sampleAnnotation is added for coordinating sample annotations on comp_heatmap
  • various anno_* helpers for each of the annotation coordinating functions above

microViz 0.8.2

Features

  • taxatree_plots can now show symbols indicating multiple levels of statistical significance
  • taxatree_plots: it is now easier to use other colour palettes with their default luminance

microViz 0.8.1

Features

  • ord_explore can perform “binary” transformations, unlocking interactive use of Binary Jaccard etc.
  • tax_transform gains add argument to simply add a constant value to all otu_table values before transformation (as an alternative to zero_replace)
  • tax_scale gains keep_counts argument for consistency with tax_transform

Fixes

  • tax_model now only requires corncob to be installed when actually used
  • ord_explore barplot numerical inputs are now debounced to prevent lag from repeated redrawing

microViz 0.8.0 - “autumn leaves”

Breaking changes

Trees

The taxatree_* family of functions are largely rewritten. For guidance, see the new website article on statistical modelling of taxa.

  • taxatree_models now attaches resulting list to ps_extra
  • taxatree_models2stats must be run on the output of taxatree_models before using taxatree_plots
  • taxatree_plots has different arguments and can now be directly labelled with taxatree_plot_labels when taxatree_label is run first to identify which taxa to label.
  • taxatree_plotkey has different arguments, with more flexible labelling conditions and a smarter label positioning approach.
  • tax_model and taxatree_models now use “lm” type by default, instead of “bbdml”, as corncob is only a suggested dependency.

Ordination

  • ord_plot default labels now have alpha = 1 for both taxa and constraints (previously 0.8)
  • ord_plot “auto”matic loading/constraint vector length scalar adjustment improvement: now uses both axes

Barplots

  • comp_barplot now uses bray-curtis by default for sample ordering (instead of aitchison) as this generally looks better
  • comp_barplot now expects palette argument colours in first-to-last order, which is more intuitive than the previous reverse order
  • distinct_palette now adds “lightgrey” to end by default

Other

  • tax_filter’s is_counts argument replaced by use_counts, allowing it to filter ps_extra objects using stored count data (i.e. after tax_transform).
  • comp_heatmap can no longer transform data internally, but accepts data already transformed with tax_transform and uses stored count data in the ps_extra for any taxa annotations
  • tax_anno heatmap annotation default style slightly changed.
  • tax_names2rank replaces deprecated tax_names2tt

Features

  • ord_plot arrow labels can now be rotated with the help of tax_lab_style() and constraint_lab_style()
  • ps_calc_dominant function added, for conveniently identifying the dominant taxon in each phyloseq sample
  • distinct_palette gains “kelly” and “greenArmytage” palettes and helpfully adds “lightgrey” to the end by default for convenient use as the palette argument to comp_barplot
  • tax_transform can now chain multiple transformations together and records these transformations in the ps_extra output
  • tax_mutate function added, for modifying the tax_table rank variables with dplyr mutate syntax
  • tax_sort can now sort ps_extra objects
  • heatmap annotation helper tax_anno no 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

Fixes

  • cor_heatmap and comp_heatmap now respect column seriation arguments when different to row seriation
  • comp_barplot now actually orders grouped samples by similarity AFTER splitting into groups, as documented

microViz 0.7.10

Updated citation information for JOSS publication. No other changes.

microViz 0.7.9

Release accompanying JOSS manuscript acceptance.

microViz 0.7.8

  • ord_plot gains vec_* helper functions for generating lists for styling taxa and constraint vectors/arrows (vec_constraint, vec_tax_all and vec_tax_sel)

microViz 0.7.7

  • ord_explore shapes selection bug fixed by limiting to 5 shapes returned by new scale_shape_girafe_filled function

microViz 0.7.6

Features

  • stat_chulls added, for drawing convex hulls on ord_plot and ord_explore ordinations
  • add_paths added, for drawing geom_paths connecting a subset of samples (over time) on an ordination plot

Fixes

  • phyloseq_validate no longer checks “unique” tax_table rank column for NAs or nchar<4 (avoiding warnings in ord_explore caused by short taxa_names)

microViz 0.7.5

  • ord_explore can now draw stat_ellipse or taxa loading vectors
  • tax_agg error messages now include personalised suggested tax_fix code

microViz 0.7.4

  • ord_explore Shiny app GUI can now also be used to interactively generate ordination plots, and to generate ord_plot code
  • ord_plot bug fix - can now plot any dimension
  • Removed deprecated tax_fill_unknowns function

microViz 0.7.3

  • phyloseq_validate verbose = FALSE is actually silent now.

microViz 0.7.2

  • ord_explore now compatible with Shiny version >=1.5.0
  • tax_fix now sends messages about fixing completely anonymous rows, instead of warnings

microViz 0.7.1

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.

microViz 0.7.0 - “fickle fixes”

Breaking changes

  • tax_fix replaces the deprecated tax_fill_unknowns, tax_fix has all the same arguments except the ‘levels’ argument, which was removed

Features

  • tax_fix_interactive Shiny app will help you clean up your taxonomy table with tax_fix

microViz 0.6.1

Breaking changes

  • ord_plot_iris and ord_explore no longer take ps argument of untransformed counts, because (by default) tax_transform now keeps the untransformed counts otu_table in the ps_extra object

Features

  • ord_explore now allows much better control over selection of points (using ggiraph functionality)
  • ord_plot now has interactive option with ggiraph package
  • ord_plot_iris gains ord_plot argument, allowing a simple pairing of iris plot and ordination to be made more easily
  • comp_barplot (and by extension ord_plot_iris) can now be made interactive in a simple fashion, using ggiraph for hover/tooltip interaction with taxa

microViz 0.6.0 - “open sesame”

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!

Breaking changes

  • tax_agg argument agg_level renamed to rank. tax_agg returns 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_unknowns x 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

Features

  • comp_barplot gets merge_other argument, which, when FALSE, shows full diversity of samples by outlining individual taxa within the (grey) “other” category!
  • tax_sort for sorting taxa in tax_table and otu_table by several name or abundance options (deletes phy_tree if present!)
  • tax_transform can 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_transform new transformation = “binary” can convert to presence/absence data (used by tax_sort for by = “prev”)
  • tax_top for flexibly returning top n taxa, at chosen rank, with ordering by tax_sort

microViz 0.5.0 - “hot maps”

Breaking changes

  • cor_heatmap and comp_heatmap argument changed: ‘taxa_which’ replaced with ‘taxa_side’ for easier control over where taxa annotations are placed (default behaviour stays the same)

Features

  • Optionally annotate cor_heatmap with variable distributions using var_anno and its helpers: anno_var_box and anno_var_hist
  • cor_heatmap gets ‘var_fun’ argument for transforming variables before correlating
  • phyloseq_validate checks for zero taxa, which can happen after filtering samples
  • tax_filter gets undetected arg (greater than), as optional alternative to prev_detection_threshold (greater than or equal to)

Bug fixes

  • heatmaps should handle NAs better (viz_heatmap internal function fix)
  • heat_palette can set range arg manually now without errors

Other

  • minor versions from 0.5 will now get a memorable name, probably referring to features added since the last minor version

microViz 0.4.3

Features

  • cor_heatmap for microbe-metadata correlation heatmaps
  • comp_heatmap for visualising taxonomic composition across samples (ordered/clustered)
  • ord_calc can now guess which method the user wants by default (by checking for presence of distance matrix and constraints)
  • ord_plot auto_caption size can now be set, and it also now exposes the coord_* args: expand and clip
  • ord_plot_iris now handles multiple rings of anno_binary annotations, and anno_binary position is now closer when no anno_colour is set
  • ord_explore shiny app menu styling is a little cleaner (but still needs some love)
  • tax_scale for applying base::scale() to phyloseq otu_table
  • tax_name for easily setting informative unique phyloseq taxa_names

Bug fixes

  • dist_permanova’s obsolete return arg removed
  • tax_filter gets explicit handling of compositional input
  • tax_fill_unknowns gets better handling of fully unclassified taxa
  • taxatree_nodes now checks for cross-rank name duplications, which would mess up the taxatree graph structure

microViz 0.4.2

Bug fixes

  • ord_explore now works with ps_extra classes
  • tax_fill_unknowns gives informative error on data with only one taxonomic rank
  • tax_filter ps argument default removed

microViz 0.4.1

Bug fixes:

  • ord_calc now correctly returns subsetted phyloseq in ps_extra obj after constrained ordination
  • taxatree_plots and taxatree_plotkey now have reactive automatic minimum node and edge sizes that depend on the set maxes

microViz 0.4.0

Breaking changes

  • dist_permanova replaces permanova for naming consistency and guiding user
  • comp_barplot replaces plot_comp_bar in anticipation of (a) future heatmap function(s) named comp_heatmap or similar

Features

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.

microViz 0.3.2

Features

  • Taxon modelling updates:
    • tax_model and taxatree_models can handle linear modeling e.g. on compositional (TS-Scaled) data
    • taxatree_plots has more sensible defaults (automatic symmetrical colour limits and variable selection based on model type)

microViz 0.3.1

Breaking changes

  • ord_plot_iris the data arg is replaced with ord and conditionally optional ps arg for when data in ord have been transformed
  • permanova always uses adonis2 now, so that arg is removed, and replaced with by argument to set sums of squares choice

Features

  • ord_plot gets a center argument to center expand the plot limits to center around zero (useful when pairing with ord_plot_iris)
  • ord_explore can now also display ordinations that don’t use distances like PCA and RDA (as well as PCoA of course)
  • ord_explore gains a ps arg (for untransformed version) and other tweaks to facilitate using transformed data in ord

Other fixes

  • ord_plot_iris annotation args are now NULL by default.
  • microbiome::aggregate_top_taxa is copied directly into microViz to avoid its coming deprecation and the current warning.

microViz 0.2.0

Features

  • taxatree_models and taxatree_plots bring tree-based visualisations of statistical models

Breaking changes

  • tax_model replaces tax_model_corncob as a function that will eventually be generalised to use other model types
  • taxatree_plots and taxatree_plotkey replaces the rudimentary taxatree_plot

microViz 0.1.2

Features

  • ord_explore allows interactive exploration of the composition of ordinated samples using Shiny

microViz 0.1.1

Features

  • ord_plot_iris for pca-ordered circular compositional barplots to pair with ord_plot output
  • ps_select for easily selecting variables within phyloseq sample data
  • ord_plot exposes scaling argument

microViz 0.1.0

Major renaming

  • calc_dist –> dist_calc
  • beta_disper –> dist_bdisp
  • ordin8 –> ord_calc
  • plot_ordin8 –> ord_plot
  • model_tax_corncob –> tax_model_corncob

Other breaking changes

  • 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

Features

  • ps_seriate for ordering phyloseq samples by similarity

microViz 0.0.6

Features

  • ps_filter allows filtering of phyloseq samples by values of variables in sample_data (wrapper around dplyr’s filter function)

Breaking changes

microViz 0.0.5

Features

  • ps_dedupe bug fix method = “readcount” now correctly keeps all samples that “first” or “last” methods do

microViz 0.0.4

Features

  • ps_arrange allows reordering of phyloseq samples by values of variables in sample_data or otu_table (wrapper around dplyr’s arrange function)
  • ps_otu2samdat add taxon abundance variables from phyloseq otu_table to sample_data for use in plotting etc

microViz 0.0.3

Features

  • ps_mutate allowing easy and piped modification of phyloseq sample_data (wrapper around dplyr’s mutate function)
  • ps_join allows easy and piped addition of a dataframe of data to phyloseq sample_data (wrapper around dplyr’s *_join functions)

microViz 0.0.2

Breaking changes

  • plot_ordin8 arguments changed to allow easier sizing and styling of all vectors and labels
  • plot_ordin8 default 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)

Other

  • ordin8 and plot_ordin8 get basic support for CCA and NMDS methods finally
  • plot_comp_bar gets order_samples_with_all_taxa and tax_transform_for_ordering
  • Documentation of manual sample ordering across plot_comp_bar groups 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.

microViz 0.0.1

Main changes

  • phyloseq_validate now fixes otu_tables stored as integers and messages user about suspicious or NA tax_table entries and this happens as part of plot_comp_bar and plot_ordin8

  • plot_comp_bar and plot_ordin8 gain taxon_renamer argument to allow you to customise the taxon names on these plots

  • plot_comp_bar can now handle missing values in the grouping variable by converting NAs to “NA”s

  • Some functions renamed for naming consistency:

    • prepend_ranks -> tax_prepend_ranks
    • tax_model_corncob -> model_tax_corncob
    • corncob_models_to_var_stats -> modelsmodels2stats_corncob
    • tax_tree_ nodes/edges/plot -> taxatree_ …

Other

  • Added a NEWS.md file to track changes to the package.