{"id":13712260,"url":"https://github.com/Hy4m/linkET","last_synced_at":"2025-05-06T21:33:39.661Z","repository":{"id":37783882,"uuid":"374377910","full_name":"Hy4m/linkET","owner":"Hy4m","description":"Everything is Linkable","archived":false,"fork":false,"pushed_at":"2023-06-14T16:16:52.000Z","size":2762,"stargazers_count":146,"open_issues_count":5,"forks_count":39,"subscribers_count":2,"default_branch":"master","last_synced_at":"2024-11-13T22:35:35.664Z","etag":null,"topics":["correlation","feature-selection","ggplot2","heatmap","r","visualization"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Hy4m.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null}},"created_at":"2021-06-06T14:14:27.000Z","updated_at":"2024-11-12T09:47:44.000Z","dependencies_parsed_at":"2024-01-07T02:00:48.354Z","dependency_job_id":null,"html_url":"https://github.com/Hy4m/linkET","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Hy4m%2FlinkET","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Hy4m%2FlinkET/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Hy4m%2FlinkET/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Hy4m%2FlinkET/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Hy4m","download_url":"https://codeload.github.com/Hy4m/linkET/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252772468,"owners_count":21801927,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["correlation","feature-selection","ggplot2","heatmap","r","visualization"],"created_at":"2024-08-02T23:01:16.472Z","updated_at":"2025-05-06T21:33:39.162Z","avatar_url":"https://github.com/Hy4m.png","language":"R","funding_links":[],"categories":["Plot layers"],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# linkET\n\n\u003c!-- badges: start --\u003e\n\u003c!-- badges: end --\u003e\n\nThe goal of `linkET` is to visualize simply and directly a matrix heatmap based\non 'ggplot2'. **Note: all functions of network have been merged in netET package.**\n\n## Installation\n\nYou can install the released version of `linkET` from [GitHub](https://github.com/) with:\n\n``` r\n# install.packages(\"devtools\")\ndevtools::install_github(\"Hy4m/linkET\", force = TRUE)\npackageVersion(\"linkET\")\n```\n## Example\n\nThis is a basic example which shows you how to solve a common problem:\n\n### Data processing\n\n```{r data_processing}\nlibrary(linkET)\n## matrix_data\nmatrix_data(list(mtcars = mtcars))\n\n## md_tbl\nmatrix_data(list(mtcars = mtcars)) %\u003e% \n  as_md_tbl()\n\n## as method\nas_matrix_data(mtcars)\n\nas_md_tbl(mtcars)\n\n## special function for correlation matrix\ncorrelate(mtcars) %\u003e% \n  as_matrix_data()\n\ncorrelate(mtcars) %\u003e% \n  as_md_tbl()\n```\n\n### Heatmap\n\n```{r heatmap}\nlibrary(ggplot2)\nmatrix_data(list(mtcars = mtcars)) %\u003e% \n  hyplot(aes(fill = mtcars)) +\n  geom_tile()\n\nas_md_tbl(mtcars) %\u003e% \n  hyplot(aes(size = mtcars)) +\n  geom_point(shape = 21, fill = NA)\n\ncorrelate(mtcars) %\u003e% \n  as_md_tbl() %\u003e% \n  qcorrplot() +\n  geom_square()\n\nlibrary(vegan)\ndata(\"varespec\")\ndata(\"varechem\")\ncorrelate(varespec[1:30], varechem) %\u003e% \n  qcorrplot() +\n  geom_square() +\n  scale_fill_gradientn(colours = RColorBrewer::brewer.pal(11, \"RdBu\"))\n\nqcorrplot(varespec[1:30], type = \"lower\") +\n  geom_square() +\n  scale_fill_gradientn(colours = RColorBrewer::brewer.pal(11, \"RdBu\"))\n\n## you can set your style\nset_corrplot_style()\nqcorrplot(mtcars) + geom_square()\n\n## reset to default style\nset_default_style()\n```\n\n## mantel test\n\n```{r mantel}\nlibrary(dplyr)\ndata(\"varechem\", package = \"vegan\")\ndata(\"varespec\", package = \"vegan\")\n\nmantel \u003c- mantel_test(varespec, varechem,\n                      spec_select = list(Spec01 = 1:7,\n                                         Spec02 = 8:18,\n                                         Spec03 = 19:37,\n                                         Spec04 = 38:44)) %\u003e% \n  mutate(rd = cut(r, breaks = c(-Inf, 0.2, 0.4, Inf),\n                  labels = c(\"\u003c 0.2\", \"0.2 - 0.4\", \"\u003e= 0.4\")),\n         pd = cut(p, breaks = c(-Inf, 0.01, 0.05, Inf),\n                  labels = c(\"\u003c 0.01\", \"0.01 - 0.05\", \"\u003e= 0.05\")))\n\nqcorrplot(correlate(varechem), type = \"lower\", diag = FALSE) +\n  geom_square() +\n  geom_couple(aes(colour = pd, size = rd), \n              data = mantel, \n              curvature = nice_curvature()) +\n  scale_fill_gradientn(colours = RColorBrewer::brewer.pal(11, \"RdBu\")) +\n  scale_size_manual(values = c(0.5, 1, 2)) +\n  scale_colour_manual(values = color_pal(3)) +\n  guides(size = guide_legend(title = \"Mantel's r\",\n                             override.aes = list(colour = \"grey35\"), \n                             order = 2),\n         colour = guide_legend(title = \"Mantel's p\", \n                               override.aes = list(size = 3), \n                               order = 1),\n         fill = guide_colorbar(title = \"Pearson's r\", order = 3))\n```\n\n## pairs plot\n\n```{r}\nqpairs(iris) + geom_pairs()\n```\n\n## Citation\n\nTo cite linkET in publications use:\n\nHouyun Huang(2021). linkET: Everything is Linkable. 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