microViz
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
파일 탐색기
최종 버전 다운로드 (.zip)- docker-publish-latest.yml
- docker-publish-release.yml
- pkgdown.yaml
- R-CMD-check.yaml
- test-coverage.yaml
- .gitignore
- ibd.rda
- shao19.rda
- Dockerfile
- Dockerfile
- CITATION
- 20210324_ord_explore_dev_x175.gif
- 20210329_ord_explore_dev_x2.gif
- logo.png
- microViz.png
- README-bars-1.png
- README-compheatmap-1.png
- README-constrained-ord-plot-1.png
- README-corheatmap-1.png
- README-ordination-plot-1.png
- add_paths.Rd
- adjacent_side.Rd
- anno_cat.Rd
- anno_cat_legend.Rd
- anno_sample.Rd
- anno_sample_cat.Rd
- anno_tax_box.Rd
- anno_tax_density.Rd
- anno_tax_prev.Rd
- anno_var_box.Rd
- anno_var_density.Rd
- anno_var_hist.Rd
- check_otutable_is_counts.Rd
- comp_barplot.Rd
- comp_heatmap.Rd
- cor_heatmap.Rd
- cor_test.Rd
- deprecated-heatmap-annotations.Rd
- dist_bdisp.Rd
- dist_calc.Rd
- dist_calc_seq.Rd
- dist_permanova.Rd
- distinct_palette.Rd
- heat_grid.Rd
- heat_numbers.Rd
- heat_palette.Rd
- ibd.Rd
- microViz.Rd
- models2stats.Rd
- new_psExtraInfo.Rd
- new_psExtraOrdInfo.Rd
- ord_arrows.Rd
- ord_calc.Rd
- ord_explore.Rd
- ord_plot-label-helpers.Rd
- ord_plot.Rd
- ord_plot_iris.Rd
- Ordination-labels.Rd
- ordination-sorting-samples.Rd
- ordination-sorting-taxa.Rd
- phyloseq_validate.Rd
- pipe.Rd
- prev.Rd
- ps_arrange.Rd
- ps_calc_diversity.Rd
- ps_calc_dominant.Rd
- ps_calc_richness.Rd
- ps_counts.Rd
- ps_dedupe.Rd
- ps_drop_incomplete.Rd
- ps_filter.Rd
- ps_join.Rd
- ps_melt.Rd
- ps_mutate.Rd
- ps_otu2samdat.Rd
- ps_reorder.Rd
- ps_select.Rd
- ps_seriate.Rd
- psExtra-accessors.Rd
- psExtra-class.Rd
- psExtraInfo.Rd
- samdatAsDataframe.Rd
- sampleAnnotation.Rd
- scale_shape_girafe_filled.Rd
- shao19.Rd
- stat_chull.Rd
- tax_agg.Rd
- tax_filter.Rd
- tax_fix.Rd
- tax_fix_interactive.Rd
- tax_model.Rd
- tax_mutate.Rd
- tax_name.Rd
- tax_names2rank.Rd
- tax_palette.Rd
- tax_palette_plot.Rd
- tax_prepend_ranks.Rd
- tax_rename.Rd
- tax_reorder.Rd
- tax_scale.Rd
- tax_select.Rd
- tax_sort.Rd
- tax_top.Rd
- tax_transform.Rd
- taxAnnotation.Rd
- taxatree_funs.Rd
- taxatree_label.Rd
- taxatree_models.Rd
- taxatree_plot_labels.Rd
- taxatree_plotkey.Rd
- taxatree_plots.Rd
- taxatree_stats_p_adjust.Rd
- taxatreePruneLabelArgs.Rd
- upgrade_ps_extra_to_psExtra.Rd
- varAnnotation.Rd
- fig1.jpg
- fig1.svg
- microViz.bib
- paper.md
- apple-touch-icon-120x120.png
- apple-touch-icon-152x152.png
- apple-touch-icon-180x180.png
- apple-touch-icon-60x60.png
- apple-touch-icon-76x76.png
- apple-touch-icon.png
- favicon-16x16.png
- favicon-32x32.png
- favicon-96x96.png
- favicon.ico
- favicon.svg
- site.webmanifest
- web-app-manifest-192x192.png
- web-app-manifest-512x512.png
- 0_onAttach.R
- add_paths.R
- check-helpers.R
- comp_barplot.R
- cor_test.R
- dist_bdisp.R
- dist_calc.R
- dist_calc_seq.R
- dist_permanova.R
- distinct_palette.R
- heatmap-utils.R
- heatmap_annotations-deprecated.R
- heatmaps-sampleAnnotation.R
- heatmaps-taxAnnotation.R
- heatmaps-varAnnotation.R
- heatmaps.R
- ibd.R
- microViz.R
- ord_arrows.R
- ord_calc.R
- ord_explore.R
- ord_labels.R
- ord_plot.R
- ord_plot_iris.R
- phyloseq_validate.R
- ps_arrange.R
- ps_calc_diversity.R
- ps_calc_dominant.R
- ps_calc_richness.R
- ps_dedupe.R
- ps_drop_incomplete.R
- ps_extra.R
- ps_filter.R
- ps_join.R
- ps_melt.R
- ps_mutate.R
- ps_otu2samdat.R
- ps_reorder.R
- ps_select.R
- ps_seriate.R
- ps_sort_ord.R
- psExtra-accessors.R
- psExtra-class.R
- scale_shape_girafe_filled.R
- seriation-helpers.R
- shao19.R
- stat_chull.R
- tax_agg.R
- tax_filter.R
- tax_fix.R
- tax_fix_interactive.R
- tax_model.R
- tax_mutate.R
- tax_name.R
- tax_names2rank.R
- tax_palette.R
- tax_prepend_ranks.R
- tax_rename.R
- tax_scale.R
- tax_select.R
- tax_sort.R
- tax_sort_ord.R
- tax_top.R
- tax_transform.R
- taxatree_funs.R
- taxatree_label.R
- taxatree_models.R
- taxatree_models2stats.R
- taxatree_plotkey.R
- taxatree_plots.R
- taxatree_stats_p_adjust.R
- utils-pipe.R
- comp-barplot.svg
- SAMPLE_order-lean.csv
- SAMPLE_order-obese.csv
- SAMPLE_order-overweight.csv
- SAMPLE_order.csv
- unique_taxa_order-lean.csv
- unique_taxa_order-obese.csv
- unique_taxa_order-overweight.csv
- unique_taxa_order.csv
- uniqueTaxonLevelsUnmerged.csv
- comp_col_order.csv
- comp_heatmap_dietswap.csv
- comp_row_order.csv
- cor_col_order.csv
- cor_col_order_v.csv
- cor_heatmap_dietswap.csv
- cor_heatmap_dietswap_v.csv
- cor_row_order.csv
- cor_row_order_v.csv
- general-ord-explore-test-001.json
- general-ord-explore-test-001_.png
- general-ord-explore-test-002.json
- general-ord-explore-test-002_.png
- general-ord-explore-test-003.json
- general-ord-explore-test-003_.png
- general-ord-explore-test-004.json
- general-ord-explore-test-004_.png
- general-ord-explore-test-005.json
- general-ord-explore-test-005_.png
- general-ord-explore-test-006.json
- general-ord-explore-test-006_.png
- general-ord-explore-test-007.json
- general-ord-explore-test-007_.png
- general-ord-explore-test-008.json
- general-ord-explore-test-008_.png
- general-ord-explore-test-009.json
- general-ord-explore-test-009_.png
- general-ord-explore-test-010.json
- general-ord-explore-test-010_.png
- general-ord-explore-test-011.json
- general-ord-explore-test-011_.png
- general-ord-explore-test-012.json
- general-ord-explore-test-012_.png
- general-ord-explore-test-001.json
- general-ord-explore-test-001_.png
- general-ord-explore-test-002.json
- general-ord-explore-test-002_.png
- general-ord-explore-test-003.json
- general-ord-explore-test-003_.png
- general-ord-explore-test-004.json
- general-ord-explore-test-004_.png
- general-ord-explore-test-005.json
- general-ord-explore-test-005_.png
- general-ord-explore-test-006.json
- general-ord-explore-test-006_.png
- general-ord-explore-test-007.json
- general-ord-explore-test-007_.png
- general-ord-explore-test-008.json
- general-ord-explore-test-008_.png
- general-ord-explore-test-009.json
- general-ord-explore-test-009_.png
- general-ord-explore-test-010.json
- general-ord-explore-test-010_.png
- general-ord-explore-test-011.json
- general-ord-explore-test-011_.png
- general-ord-explore-test-012.json
- general-ord-explore-test-012_.png
- 001.json
- 001_.png
- 002.json
- 002_.png
- 003.json
- 003_.png
- 004.json
- 004_.png
- 005.json
- 005_.png
- general-ord-explore-test-001.json
- general-ord-explore-test-001_.png
- general-ord-explore-test-002.json
- general-ord-explore-test-002_.png
- general-ord-explore-test-003.json
- general-ord-explore-test-003_.png
- general-ord-explore-test-004.json
- general-ord-explore-test-004_.png
- general-ord-explore-test-005.json
- general-ord-explore-test-005_.png
- general-ord-explore-test-006.json
- general-ord-explore-test-006_.png
- general-ord-explore-test-007.json
- general-ord-explore-test-007_.png
- general-ord-explore-test-008.json
- general-ord-explore-test-008_.png
- general-ord-explore-test-009.json
- general-ord-explore-test-009_.png
- general-ord-explore-test-010.json
- general-ord-explore-test-010_.png
- general-ord-explore-test-011.json
- general-ord-explore-test-011_.png
- general-ord-explore-test-012.json
- general-ord-explore-test-012_.png
- 001.json
- 001_.png
- 002.json
- 002_.png
- 003.json
- 003_.png
- 004.json
- 004_.png
- 005.json
- 005_.png
- dietDistsAll.csv
- dietDistsNoTree.csv
- esoDistsAll.csv
- esoDistsNoTree.csv
- taxa-names.csv
- constrained-custom-labels.svg
- unconstrained-rotated-labels.svg
- rda-triplot.svg
- diversity-pca.svg
- dominant-taxa-pca.svg
- richness-pca.svg
- dedupe_group.csv
- dedupe_readcount.csv
- melted_ps.csv
- otu.csv
- tt.csv
- enterotype.csv
- fixed_enterotype.csv
- fixed_ibd.csv
- fixed_modified_dietswap.csv
- ibd.csv
- modified_dietswap.csv
- tax_common_unknowns-0.csv
- tax_common_unknowns-1.csv
- tax_common_unknowns-2.csv
- tax_common_unknowns-3.csv
- tax_common_unknowns-4.csv
- tax_common_unknowns-5.csv
- ps1-names.csv
- ps2-names.csv
- tax-palette-plot.svg
- ibd_phylo_names.csv
- ibd_renamed.csv
- ibd_renamed_2.csv
- ibd_renamed_max.csv
- tax_top.csv
- diet_fam_bin10.csv
- diet_fam_clr.csv
- diet_fam_clr2.csv
- diet_fam_l10p.csv
- diet_fam_l2p.csv
- diet_fam_prop.csv
- diet_fam_rclr.csv
- trans-chaining.svg
- lmBirthweight_psx.csv
- wilcox2_psx.csv
- taxatreekey-multiplelabels.csv
- unlabeledKey_rectData.csv
- unlabeledKeyData.csv
- taxatree-plot-age-m.svg
- taxatree-plot-age.svg
- taxatree-plot-uc-m.svg
- taxatree-plot-uc.svg
- taxatree_plotkey-before-stats.csv
- comp_barplot.md
- dist_calc.md
- heatmaps.md
- ord_arrows.md
- ord_explore-shinytest2.md
- ord_explore.md
- ord_plot.md
- phyloseq_validate.md
- ps_calc_richness.md
- ps_join.md
- tax_agg.md
- tax_fix.md
- tax_fix_interactive.md
- tax_sort.md
- tax_transform.md
- taxatree_models2stats.md
- taxatree_plotkey.md
- helper-microViz-tests.R
- test-comp_barplot.R
- test-dist_bdisp.R
- test-dist_calc.R
- test-heatmaps.R
- test-ord_arrows.R
- test-ord_calc.R
- test-ord_explore-shinytest2.R
- test-ord_explore.R
- test-ord_labels.R
- test-ord_plot.R
- test-ord_plot_iris.R
- test-permanova.R
- test-phyloseq_validate.R
- test-ps_arrange.R
- test-ps_calc_diversity.R
- test-ps_calc_dominant.R
- test-ps_calc_richness.R
- test-ps_dedupe.R
- test-ps_extra-accessors.R
- test-ps_filter.R
- test-ps_join.R
- test-ps_melt.R
- test-ps_otu2samdat.R
- test-ps_select.R
- test-scale_shape_girafe_filled.R
- test-tax_agg.R
- test-tax_fix.R
- test-tax_fix_interactive.R
- test-tax_model.R
- test-tax_mutate.R
- test-tax_name.R
- test-tax_palette.R
- test-tax_rename.R
- test-tax_select.R
- test-tax_sort.R
- test-tax_top.R
- test-tax_transform.R
- test-taxatree_models2stats.R
- test-taxatree_plotkey.R
- test-taxatree_plots.R
- testthat.R
- ord_explore.gif
- microViz.Rmd
- ps_extra-replaced.Rmd
- shao19-analyses.Rmd
- exercises.Rmd
- 20210329_ord_explore_dev_x2.gif
- 20210411_tax_fix_interactive_x2.gif
- 20210429_ord_explore_x175.gif
- atlas1006.Rmd
- compositions.Rmd
- heatmaps.Rmd
- modelling-taxa.Rmd
- ordination-interactive.Rmd
- ordination.Rmd
- phyloseq.Rmd
- tax-fixing.Rmd
- videos.Rmd
- .gitignore
- .gitignore
- .Rbuildignore
- _pkgdown.yml
- CODE_OF_CONDUCT.md
- DESCRIPTION
- LICENSE.md
- microViz.Rproj
- NAMESPACE
- NEWS.md
- README.md
- README.Rmd
# 설치 가이드
1. 코드 내려받기
git clone https://github.com/david-barnett/microViz
깃허브에서 프로젝트 코드 전체를 내 컴퓨터로 내려받습니다.
cd microViz
방금 내려받은 프로젝트 폴더 안으로 이동합니다.
2. Docker
쉬움 추천사전 준비물
- Git GitHub에서 프로젝트 코드를 내려받으려면 필요합니다.
- Docker Desktop 컨테이너를 빌드하고 실행하려면 필요합니다. 설치 후 실행해서 백그라운드에 켜두세요.
:whale: For Docker users an image with the main branch installed is
이 명령어를 터미널에 그대로 입력해 실행하세요.
<https://hub.docker.com/r/barnettdavid/microviz-rocker-verse>
이 명령어를 터미널에 그대로 입력해 실행하세요.
터미널에 docker compose ps 를 입력해 컨테이너들이 Up 상태인지 확인하세요. README에 포트 번호가 적혀있다면 브라우저에서 http://localhost:포트번호 로 접속해보세요.
이 레포의 README에 적힌 실제 명령어를 그대로 가져왔습니다.
// repository documentation
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