Package: microViz 0.13.2

microViz: Microbiome Data Analysis and Visualization

Microbiome data visualization and statistics tools built upon phyloseq.

Authors:David Barnett [aut, cre]

microViz_0.13.2.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
microViz/json (API)

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

Bug tracker:https://github.com/david-barnett/microviz/issues

Pkgdown/docs site:https://david-barnett.github.io

Datasets:
  • ibd - IBD study data in phyloseq object.
  • shao19 - Gut microbiota relative abundance data from Shao et al. 2019

On CRAN:

Conda:

microbiomemicrobiome-analysismicrobiota

6.74 score 128 stars 1.1k scripts 108 exports 125 dependencies

Last updated from:0a2c3f95e7. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK490
source / vignettesOK540
linux-releaseOK564
macos-releaseOK307
macos-oldrelOK437
windows-develOK503
windows-releaseOK333
windows-oldrelOK434
wasm-releaseOK163

Exports:%>%add_pathsadjacent_sideanno_abundanno_catanno_cat_legendanno_prevanno_sampleanno_sample_catanno_tax_boxanno_tax_densityanno_tax_prevanno_var_boxanno_var_densityanno_var_histbdisp_getcomp_barplotcomp_heatmapconstraint_lab_stylecor_heatmapcor_testdist_bdispdist_calcdist_calc_seqdist_getdist_permanovadistinct_paletteheat_gridheat_numbersheat_paletteinfo_getold_anno_var_boxold_anno_var_histord_calcord_exploreord_getord_order_samplesord_plotord_plot_irisotu_getperm_getphyloseq_validateprevps_arrangeps_calc_diversityps_calc_dominantps_calc_richnessps_dedupeps_drop_incompleteps_filterps_getps_joinps_meltps_mutateps_otu2samdatps_reorderps_selectps_seriateps_sort_ordsamdat_tblsampleAnnotationscale_shape_girafe_filledstat_chulltax_aggtax_annotax_filtertax_fixtax_fix_interactivetax_lab_styletax_modeltax_models_gettax_models2statstax_mutatetax_nametax_names2ranktax_palettetax_palette_plottax_prepend_rankstax_renametax_reordertax_scaletax_selecttax_sorttax_sort_ordtax_stats_gettax_toptax_transformtaxAnnotationtaxatree_edgestaxatree_labeltaxatree_modelstaxatree_models_gettaxatree_models2statstaxatree_nodestaxatree_plot_labelstaxatree_plotkeytaxatree_plotstaxatree_stats_gettaxatree_stats_p_adjusttextAngleCalctextHjustCalctt_getupgrade_ps_extra_to_psExtravar_annovarAnnotationvec_constraintvec_tax_allvec_tax_sel

Dependencies:ade4apebackportsbase64encbayesmBiobaseBiocGenericsbiomformatBiostringsbroombslibcacachemcirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcompositionscowplotcpp11crayondata.tableDEoptimRdigestdoParalleldplyrevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforeachfsgclusgdtoolsgenericsGetoptLongggiraphggplot2GlobalOptionsgluegtablehighrhtmltoolshtmlwidgetshttpuvigraphIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelifecyclemagrittrMASSMatrixmatrixStatsmemoisemgcvmicrobiomemimemulttestnlmeotelpermutephyloseqpillarpixmappkgconfigplyrpngpromisespurrrqapR6rappdirsRColorBrewerRcppRcppArmadilloregistryreshape2rjsonrlangrmarkdownrobustbaseRtsneS4VectorsS7sassscalesSeqinfoseriationshapeshinysourcetoolsspstringistringrsurvivalsystemfontstensorAtibbletidyrtidyselecttinytexTSPutf8vctrsveganviridisLitewithrxfunxtableXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Add paths connecting points on a ggplot scatterplotadd_paths
Simple heatmap helper to get a default adjacent side for another annotationadjacent_side
Create colored rectangle annotations for categorical dataanno_cat
Convenience function for generating a legend for anno_cat annotations.anno_cat_legend
Helper to specify simple comp_heatmap annotation for other sample dataanno_sample
Helper to specify comp_heatmap annotation for categorical sample dataanno_sample_cat
Helper to specify heatmap annotation for showing taxa abundance on boxplotanno_tax_box
Helper to specify heatmap annotation for showing taxa abundance density plotanno_tax_density
Helper to specify heatmap annotation for showing taxa prevalence as barplotanno_tax_prev
Helper to specify heatmap annotation for variable distribution boxplotsanno_var_box
Helper to specify heatmap annotation for variable distribution density plotanno_var_density
Helper to specify heatmap annotation for variable distribution histogramsanno_var_hist
Plot (grouped and ordered) compositional barplotscomp_barplot
Draw heatmap of microbiome composition across samplescomp_heatmap
Microbe-to-sample-data correlation heatmapcor_heatmap
Simple wrapper around cor.test for y ~ x style formula inputcor_test
DEPRECATED Heatmap annotations helpersanno_abund anno_prev deprecated-heatmap-annotations old_anno_var_box old_anno_var_hist tax_anno var_anno
Wrapper for vegan::betadisper()dist_bdisp
Calculate distances between pairs of samples in phyloseq objectdist_calc
Calculate distances between sequential samples in ps_extra/phyloseq objectdist_calc_seq
Calculate PERMANOVA after dist_calc()dist_permanova
Colour palettes suitable for 20+ categoriesdistinct_palette
set options for drawing gridlines on heatmapsheat_grid
Aesthetic settings for drawing numbers on heatmap tilesheat_numbers
Easy palettes for ComplexHeatmapheat_palette
IBD study data in phyloseq object.ibd
microViz: microbiome data analysis and visualizationmicroViz-package microViz
Ordinate samples (arrange by similarity in multiple dimensions)ord_calc
Interactively explore microbial compositions of ordinated samplesord_explore
Customisable ggplot2 ordination plotord_plot
Circular compositional barplot sorted by ordination angleord_plot_iris
Create ordination plot vector styling listsOrdination-arrows vec_constraint vec_tax_all vec_tax_sel
Create list for ord_plot() *_lab_style argumentsconstraint_lab_style Ordination-labels tax_lab_style
Check for (and fix) common problems with phyloseq objectsphyloseq_validate
Calculate prevalence from numeric vectorprev
Print method for psExtraInfo objectprint.psExtraInfo
Arrange samples in phyloseq by sample_data variables or taxon abundanceps_arrange
Calculate diversity index and add to phyloseq sample dataps_calc_diversity
Calculate dominant taxon in each phyloseq sampleps_calc_dominant
Calculate richness estimate and add to phyloseq sample dataps_calc_richness
De-duplicate phyloseq samplesps_dedupe
Deselect phyloseq samples with sample_data missingsps_drop_incomplete
Filter phyloseq samples by sample_data variablesps_filter
Join a dataframe to phyloseq sample dataps_join
Melt phyloseq data object into large data.frame (tibble)ps_melt
Modify or compute new sample_data in phyloseq objectps_mutate
Copy phyloseq otu_table data to sample_dataps_otu2samdat
Set order of samples in phyloseq objectps_reorder
Select phyloseq sample_data using dplyr::select syntaxps_select
Arrange samples in a phyloseq by microbiome similarityps_seriate
Sort phyloseq samples by ordination axes scoresord_order_samples ps_sort_ord
Extract elements from psExtra classbdisp_get dist_get info_get ord_get otu_get perm_get psExtra-accessors ps_get samdat_tbl taxatree_models_get taxatree_stats_get tax_models_get tax_stats_get tt_get
Define psExtra class S4 objectpsExtra-class
Helper to specify a HeatmapAnnotation for samples in comp_heatmapsampleAnnotation
Filled shapes for ggiraph interactive plotsscale_shape_girafe_filled
Gut microbiota relative abundance data from Shao et al. 2019shao19
Draw convex hull for a set of points on a ggplotstat_chull
Aggregate taxa and track aggregation in psExtratax_agg
Filter rare and/or low abundance taxa from a phyloseq objecttax_filter
Replace unknown, NA, or short tax_table valuestax_fix
Shiny app to help you use tax_fixtax_fix_interactive
Statistical modelling for individual taxa in a phyloseqtax_model
Modify or compute new taxonomic ranks in phyloseqtax_mutate
Simple way to set unique taxa_names for phyloseq objecttax_name
Add taxa_names as last column in phyloseq tax_tabletax_names2rank
Make a fixed taxa colour palette e.g. for comp_barplottax_palette
tax_palette plotting helper functiontax_palette_plot
Add rank prefixes to phyloseq tax_table valuestax_prepend_ranks
Make new phyloseq taxa names from classification and taxon abundance infotax_rename
Reorder taxa in phyloseq object using vector of namestax_reorder
Mean-center and SD-scale taxa in phyloseqtax_scale
Subset phyloseq object by (partial) taxa namestax_select
Sort taxa in phyloseq otu_table and tax_tabletax_sort
Order taxa in phyloseq by their loading vectorsord_order_taxa tax_sort_ord
Get names of "top" n taxatax_top
Transform taxa in phyloseq object and record transformationtax_transform
Helper to specify a HeatmapAnnotation for taxataxAnnotation
Create node and edge dataframes for taxatree_plotstaxatree_edges taxatree_funs taxatree_nodes
Add logical label column to taxatree_stats dataframetaxatree_label
Statistical modelling for individual taxa across multiple rankstaxatree_models
Extract statistics from taxatree_models or tax_model outputtaxatree_models2stats tax_models2stats
Add labels to taxatree plots/keytaxatree_plot_labels
Draw labelled key to accompany taxatree_plotstaxatree_plotkey
Plot statistical model results for all taxa on a taxonomic treetaxatree_plots
Adjust p values in taxatree_stats dataframetaxatree_stats_p_adjust
Convert old format "ps_extra" objects to new "psExtra" objectsupgrade_ps_extra_to_psExtra
Helper to specify a HeatmapAnnotation for variables in cor_heatmapvarAnnotation