Files in david-barnett/microViz
Microbiome Data Analysis and Visualization

.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/docker-publish-latest.yml
.github/workflows/docker-publish-release.yml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
CODE_OF_CONDUCT.md
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md R/0_onAttach.R R/add_paths.R R/check-helpers.R R/comp_barplot.R R/cor_test.R R/dist_bdisp.R R/dist_calc.R R/dist_calc_seq.R R/dist_permanova.R R/distinct_palette.R R/heatmap-utils.R R/heatmap_annotations-deprecated.R R/heatmaps-sampleAnnotation.R R/heatmaps-taxAnnotation.R R/heatmaps-varAnnotation.R R/heatmaps.R R/ibd.R R/microViz.R R/ord_arrows.R R/ord_calc.R R/ord_explore.R R/ord_labels.R R/ord_plot.R R/ord_plot_iris.R R/phyloseq_validate.R R/psExtra-accessors.R R/psExtra-class.R R/ps_arrange.R R/ps_calc_diversity.R R/ps_calc_dominant.R R/ps_calc_richness.R R/ps_dedupe.R R/ps_drop_incomplete.R R/ps_extra.R R/ps_filter.R R/ps_join.R R/ps_melt.R R/ps_mutate.R R/ps_otu2samdat.R R/ps_reorder.R R/ps_select.R R/ps_seriate.R R/ps_sort_ord.R R/scale_shape_girafe_filled.R R/seriation-helpers.R R/shao19.R R/stat_chull.R R/tax_agg.R R/tax_filter.R R/tax_fix.R R/tax_fix_interactive.R R/tax_model.R R/tax_mutate.R R/tax_name.R R/tax_names2rank.R R/tax_palette.R R/tax_prepend_ranks.R R/tax_rename.R R/tax_scale.R R/tax_select.R R/tax_sort.R R/tax_sort_ord.R R/tax_top.R R/tax_transform.R R/taxatree_funs.R R/taxatree_label.R R/taxatree_models.R R/taxatree_models2stats.R R/taxatree_plotkey.R R/taxatree_plots.R R/taxatree_stats_p_adjust.R R/utils-pipe.R README.Rmd README.md
_pkgdown.yml
data/ibd.rda
data/shao19.rda
docker/latest/Dockerfile
docker/release/Dockerfile
inst/CITATION
man/Ordination-labels.Rd man/add_paths.Rd man/adjacent_side.Rd man/anno_cat.Rd man/anno_cat_legend.Rd man/anno_sample.Rd man/anno_sample_cat.Rd man/anno_tax_box.Rd man/anno_tax_density.Rd man/anno_tax_prev.Rd man/anno_var_box.Rd man/anno_var_density.Rd man/anno_var_hist.Rd man/check_otutable_is_counts.Rd man/comp_barplot.Rd man/comp_heatmap.Rd man/cor_heatmap.Rd man/cor_test.Rd man/deprecated-heatmap-annotations.Rd man/dist_bdisp.Rd man/dist_calc.Rd man/dist_calc_seq.Rd man/dist_permanova.Rd man/distinct_palette.Rd
man/figures/20210324_ord_explore_dev_x175.gif
man/figures/20210329_ord_explore_dev_x2.gif
man/figures/README-bars-1.png
man/figures/README-compheatmap-1.png
man/figures/README-constrained-ord-plot-1.png
man/figures/README-corheatmap-1.png
man/figures/README-ordination-plot-1.png
man/figures/logo.png
man/figures/microViz.png
man/heat_grid.Rd man/heat_numbers.Rd man/heat_palette.Rd man/ibd.Rd man/microViz.Rd man/models2stats.Rd man/new_psExtraInfo.Rd man/new_psExtraOrdInfo.Rd man/ord_arrows.Rd man/ord_calc.Rd man/ord_explore.Rd man/ord_plot-label-helpers.Rd man/ord_plot.Rd man/ord_plot_iris.Rd man/ordination-sorting-samples.Rd man/ordination-sorting-taxa.Rd man/phyloseq_validate.Rd man/pipe.Rd man/prev.Rd man/psExtra-accessors.Rd man/psExtra-class.Rd man/psExtraInfo.Rd man/ps_arrange.Rd man/ps_calc_diversity.Rd man/ps_calc_dominant.Rd man/ps_calc_richness.Rd man/ps_counts.Rd man/ps_dedupe.Rd man/ps_drop_incomplete.Rd man/ps_filter.Rd man/ps_join.Rd man/ps_melt.Rd man/ps_mutate.Rd man/ps_otu2samdat.Rd man/ps_reorder.Rd man/ps_select.Rd man/ps_seriate.Rd man/samdatAsDataframe.Rd man/sampleAnnotation.Rd man/scale_shape_girafe_filled.Rd man/shao19.Rd man/stat_chull.Rd man/taxAnnotation.Rd man/tax_agg.Rd man/tax_filter.Rd man/tax_fix.Rd man/tax_fix_interactive.Rd man/tax_model.Rd man/tax_mutate.Rd man/tax_name.Rd man/tax_names2rank.Rd man/tax_palette.Rd man/tax_palette_plot.Rd man/tax_prepend_ranks.Rd man/tax_rename.Rd man/tax_reorder.Rd man/tax_scale.Rd man/tax_select.Rd man/tax_sort.Rd man/tax_top.Rd man/tax_transform.Rd man/taxatreePruneLabelArgs.Rd man/taxatree_funs.Rd man/taxatree_label.Rd man/taxatree_models.Rd man/taxatree_plot_labels.Rd man/taxatree_plotkey.Rd man/taxatree_plots.Rd man/taxatree_stats_p_adjust.Rd man/upgrade_ps_extra_to_psExtra.Rd man/varAnnotation.Rd
manuscript/fig1.jpg
manuscript/fig1.svg
manuscript/microViz.bib
manuscript/paper.md
microViz.Rproj
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon-96x96.png
pkgdown/favicon/favicon.ico
pkgdown/favicon/favicon.svg
pkgdown/favicon/site.webmanifest
pkgdown/favicon/web-app-manifest-192x192.png
pkgdown/favicon/web-app-manifest-512x512.png
tests/testthat.R tests/testthat/_snaps/comp_barplot.md
tests/testthat/_snaps/comp_barplot/SAMPLE_order-lean.csv
tests/testthat/_snaps/comp_barplot/SAMPLE_order-obese.csv
tests/testthat/_snaps/comp_barplot/SAMPLE_order-overweight.csv
tests/testthat/_snaps/comp_barplot/SAMPLE_order.csv
tests/testthat/_snaps/comp_barplot/comp-barplot.svg
tests/testthat/_snaps/comp_barplot/uniqueTaxonLevelsUnmerged.csv
tests/testthat/_snaps/comp_barplot/unique_taxa_order-lean.csv
tests/testthat/_snaps/comp_barplot/unique_taxa_order-obese.csv
tests/testthat/_snaps/comp_barplot/unique_taxa_order-overweight.csv
tests/testthat/_snaps/comp_barplot/unique_taxa_order.csv
tests/testthat/_snaps/dist_calc.md tests/testthat/_snaps/heatmaps.md
tests/testthat/_snaps/heatmaps/comp_col_order.csv
tests/testthat/_snaps/heatmaps/comp_heatmap_dietswap.csv
tests/testthat/_snaps/heatmaps/comp_row_order.csv
tests/testthat/_snaps/heatmaps/cor_col_order.csv
tests/testthat/_snaps/heatmaps/cor_col_order_v.csv
tests/testthat/_snaps/heatmaps/cor_heatmap_dietswap.csv
tests/testthat/_snaps/heatmaps/cor_heatmap_dietswap_v.csv
tests/testthat/_snaps/heatmaps/cor_row_order.csv
tests/testthat/_snaps/heatmaps/cor_row_order_v.csv
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-001.json
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-001_.png
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-002.json
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-002_.png
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-003.json
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-003_.png
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-004.json
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-004_.png
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-005.json
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-005_.png
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-006.json
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-006_.png
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-007.json
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-007_.png
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-008.json
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-008_.png
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-009.json
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-009_.png
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-010.json
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-010_.png
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-011.json
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-011_.png
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-012.json
tests/testthat/_snaps/mac-4.4/ord_explore-shinytest2/general-ord-explore-test-012_.png
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-001.json
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-001_.png
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-002.json
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-002_.png
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-003.json
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-003_.png
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-004.json
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-004_.png
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-005.json
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-005_.png
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-006.json
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-006_.png
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-007.json
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-007_.png
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-008.json
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-008_.png
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-009.json
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-009_.png
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-010.json
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-010_.png
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-011.json
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-011_.png
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-012.json
tests/testthat/_snaps/mac-4.5/ord_explore-shinytest2/general-ord-explore-test-012_.png
tests/testthat/_snaps/mac-4.5/tax_fix_interactive/001.json
tests/testthat/_snaps/mac-4.5/tax_fix_interactive/001_.png
tests/testthat/_snaps/mac-4.5/tax_fix_interactive/002.json
tests/testthat/_snaps/mac-4.5/tax_fix_interactive/002_.png
tests/testthat/_snaps/mac-4.5/tax_fix_interactive/003.json
tests/testthat/_snaps/mac-4.5/tax_fix_interactive/003_.png
tests/testthat/_snaps/mac-4.5/tax_fix_interactive/004.json
tests/testthat/_snaps/mac-4.5/tax_fix_interactive/004_.png
tests/testthat/_snaps/mac-4.5/tax_fix_interactive/005.json
tests/testthat/_snaps/mac-4.5/tax_fix_interactive/005_.png
tests/testthat/_snaps/ord_arrows.md tests/testthat/_snaps/ord_explore-shinytest2.md
tests/testthat/_snaps/ord_explore-shinytest2/taxa-names.csv
tests/testthat/_snaps/ord_explore.md
tests/testthat/_snaps/ord_explore/dietDistsAll.csv
tests/testthat/_snaps/ord_explore/dietDistsNoTree.csv
tests/testthat/_snaps/ord_explore/esoDistsAll.csv
tests/testthat/_snaps/ord_explore/esoDistsNoTree.csv
tests/testthat/_snaps/ord_labels/constrained-custom-labels.svg
tests/testthat/_snaps/ord_labels/unconstrained-rotated-labels.svg
tests/testthat/_snaps/ord_plot.md
tests/testthat/_snaps/ord_plot/rda-triplot.svg
tests/testthat/_snaps/phyloseq_validate.md
tests/testthat/_snaps/ps_calc_diversity/diversity-pca.svg
tests/testthat/_snaps/ps_calc_dominant/dominant-taxa-pca.svg
tests/testthat/_snaps/ps_calc_richness.md
tests/testthat/_snaps/ps_calc_richness/richness-pca.svg
tests/testthat/_snaps/ps_dedupe/dedupe_group.csv
tests/testthat/_snaps/ps_dedupe/dedupe_readcount.csv
tests/testthat/_snaps/ps_join.md
tests/testthat/_snaps/ps_melt/melted_ps.csv
tests/testthat/_snaps/tax_agg.md
tests/testthat/_snaps/tax_agg/otu.csv
tests/testthat/_snaps/tax_agg/tt.csv
tests/testthat/_snaps/tax_fix.md
tests/testthat/_snaps/tax_fix/enterotype.csv
tests/testthat/_snaps/tax_fix/fixed_enterotype.csv
tests/testthat/_snaps/tax_fix/fixed_ibd.csv
tests/testthat/_snaps/tax_fix/fixed_modified_dietswap.csv
tests/testthat/_snaps/tax_fix/ibd.csv
tests/testthat/_snaps/tax_fix/modified_dietswap.csv
tests/testthat/_snaps/tax_fix/tax_common_unknowns-0.csv
tests/testthat/_snaps/tax_fix/tax_common_unknowns-1.csv
tests/testthat/_snaps/tax_fix/tax_common_unknowns-2.csv
tests/testthat/_snaps/tax_fix/tax_common_unknowns-3.csv
tests/testthat/_snaps/tax_fix/tax_common_unknowns-4.csv
tests/testthat/_snaps/tax_fix/tax_common_unknowns-5.csv
tests/testthat/_snaps/tax_fix_interactive.md
tests/testthat/_snaps/tax_name/ps1-names.csv
tests/testthat/_snaps/tax_name/ps2-names.csv
tests/testthat/_snaps/tax_palette/tax-palette-plot.svg
tests/testthat/_snaps/tax_rename/ibd_phylo_names.csv
tests/testthat/_snaps/tax_rename/ibd_renamed.csv
tests/testthat/_snaps/tax_rename/ibd_renamed_2.csv
tests/testthat/_snaps/tax_rename/ibd_renamed_max.csv
tests/testthat/_snaps/tax_sort.md
tests/testthat/_snaps/tax_top/tax_top.csv
tests/testthat/_snaps/tax_transform.md
tests/testthat/_snaps/tax_transform/diet_fam_bin10.csv
tests/testthat/_snaps/tax_transform/diet_fam_clr.csv
tests/testthat/_snaps/tax_transform/diet_fam_l10p.csv
tests/testthat/_snaps/tax_transform/diet_fam_l2p.csv
tests/testthat/_snaps/tax_transform/diet_fam_prop.csv
tests/testthat/_snaps/tax_transform/diet_fam_rclr.csv
tests/testthat/_snaps/tax_transform/trans-chaining.svg
tests/testthat/_snaps/taxatree_models2stats.md
tests/testthat/_snaps/taxatree_models2stats/lmBirthweight_psx.csv
tests/testthat/_snaps/taxatree_models2stats/wilcox2_psx.csv
tests/testthat/_snaps/taxatree_plotkey.md
tests/testthat/_snaps/taxatree_plotkey/taxatreekey-multiplelabels.csv
tests/testthat/_snaps/taxatree_plotkey/unlabeledKeyData.csv
tests/testthat/_snaps/taxatree_plotkey/unlabeledKey_rectData.csv
tests/testthat/_snaps/taxatree_plots/taxatree-plot-age-m.svg
tests/testthat/_snaps/taxatree_plots/taxatree-plot-age.svg
tests/testthat/_snaps/taxatree_plots/taxatree-plot-uc-m.svg
tests/testthat/_snaps/taxatree_plots/taxatree-plot-uc.svg
tests/testthat/_snaps/taxatree_plots/taxatree_plotkey-before-stats.csv
tests/testthat/helper-microViz-tests.R tests/testthat/test-comp_barplot.R tests/testthat/test-dist_calc.R tests/testthat/test-heatmaps.R tests/testthat/test-ord_arrows.R tests/testthat/test-ord_calc.R tests/testthat/test-ord_explore-shinytest2.R tests/testthat/test-ord_explore.R tests/testthat/test-ord_labels.R tests/testthat/test-ord_plot.R tests/testthat/test-ord_plot_iris.R tests/testthat/test-permanova.R tests/testthat/test-phyloseq_validate.R tests/testthat/test-ps_arrange.R tests/testthat/test-ps_calc_diversity.R tests/testthat/test-ps_calc_dominant.R tests/testthat/test-ps_calc_richness.R tests/testthat/test-ps_dedupe.R tests/testthat/test-ps_extra-accessors.R tests/testthat/test-ps_filter.R tests/testthat/test-ps_join.R tests/testthat/test-ps_melt.R tests/testthat/test-ps_otu2samdat.R tests/testthat/test-ps_select.R tests/testthat/test-scale_shape_girafe_filled.R tests/testthat/test-tax_agg.R tests/testthat/test-tax_fix.R tests/testthat/test-tax_fix_interactive.R tests/testthat/test-tax_model.R tests/testthat/test-tax_mutate.R tests/testthat/test-tax_name.R tests/testthat/test-tax_palette.R tests/testthat/test-tax_rename.R tests/testthat/test-tax_select.R tests/testthat/test-tax_sort.R tests/testthat/test-tax_top.R tests/testthat/test-tax_transform.R tests/testthat/test-taxatree_models2stats.R tests/testthat/test-taxatree_plotkey.R tests/testthat/test-taxatree_plots.R
vignettes/.gitignore
vignettes/articles/assets/ord_explore.gif
vignettes/articles/microViz.Rmd vignettes/articles/ps_extra-replaced.Rmd vignettes/articles/shao19-analyses.Rmd vignettes/learn/exercises.Rmd vignettes/web-only/atlas1006.Rmd vignettes/web-only/compositions.Rmd vignettes/web-only/heatmaps.Rmd
vignettes/web-only/images/20210329_ord_explore_dev_x2.gif
vignettes/web-only/images/20210411_tax_fix_interactive_x2.gif
vignettes/web-only/images/20210429_ord_explore_x175.gif
vignettes/web-only/modelling-taxa.Rmd vignettes/web-only/ordination-interactive.Rmd vignettes/web-only/ordination.Rmd vignettes/web-only/phyloseq.Rmd vignettes/web-only/tax-fixing.Rmd vignettes/web-only/videos.Rmd
david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.