{"Package":"ggalign","Title":"A 'ggplot2' Extension for Consistent Axis Alignment","Version":"0.0.4","Authors@R":"person(\"Yun\", \"Peng\", , \"yunyunp96@163.com\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0003-2801-3332\"))","Description":"A 'ggplot2' extension offers various tools for organizing and arranging plots.\nIt is designed to consistently align a specific axis across multiple 'ggplot' objects,\nmaking it especially useful for plots requiring data order manipulation. A typical use\ncase includes organizing combinations like a dendrogram and a heatmap.","License":"MIT + file LICENSE","URL":"https://github.com/Yunuuuu/ggalign,\nhttps://yunuuuu.github.io/ggalign/","BugReports":"https://github.com/Yunuuuu/ggalign/issues","Depends":"ggplot2 (>= 3.3.0)","Imports":"cli, data.table, grid, gtable, methods, rlang (>= 1.1.0),\nstats, utils, vctrs","Suggests":"bookdown, ggrastr, gridGraphics, knitr, patchwork, ragg,\nrmarkdown, scales, seriation, testthat (>= 3.0.0), vdiffr","ByteCompile":"true","Config/testthat/edition":"3","Encoding":"UTF-8","RoxygenNote":"7.3.2","VignetteBuilder":"knitr","NeedsCompilation":"no","Packaged":"2024-10-12 12:17:14 UTC; yun","Author":"Yun Peng [aut, cre, cph] ()","Maintainer":"Yun Peng ","Repository":"CRAN","Date/Publication":"2024-10-12 13:10:02 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/ggalign_0.0.4.tar.gz","jsonAuthors":[{"name":"Yun Peng","email":"yunyunp96@163.com","maintainer":true}],"readme":"\n\n\n# ggalign $\"ggalign$ \n\n\n\n[![R-CMD-check](https://github.com/Yunuuuu/ggalign/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Yunuuuu/ggalign/actions/workflows/R-CMD-check.yaml)\n[![Codecov test\ncoverage](https://codecov.io/gh/Yunuuuu/ggalign/branch/main/graph/badge.svg)](https://app.codecov.io/gh/Yunuuuu/ggalign?branch=main)\n[![CRAN\nstatus](https://www.r-pkg.org/badges/version/ggalign)](https://CRAN.R-project.org/package=ggalign)\n\n\nThis package extends ggplot2 by providing advanced tools for aligning\nand organizing multiple plots, particularly those that automatically\nreorder observations, such as dendrogram. It offers fine control over\nlayout adjustment and plot annotations, enabling you to create complex,\npublication-quality visualizations while still using the familiar\ngrammar of ggplot2.\n\n## Why use `ggalign`?\n\n`ggalign` focuses on aligning observations across multiple plots. It\nleverages the `\"number of observations\"` in the\n[vctrs](https://vctrs.r-lib.org/reference/vec_size.html) package or\n`NROW()` function to maintain consistency in plot organization.\n\nIf you’ve ever struggled with aligning plots with self-contained\nordering (like dendrogram), or applying consistent grouping or ordering\nacross multiple plots (e.g., with k-means clustering), `ggalign` is\ndesigned to make this easier. The package integrates seamlessly with\nggplot2, providing the flexibility to use its geoms, scales, and other\ncomponents for complex visualizations.\n\n## Installation\n\nYou can install `ggalign` from `CRAN` using:\n\n``` r\ninstall.packages(\"ggalign\")\n```\n\nAlternatively, install the development version from\n[GitHub](https://github.com/Yunuuuu/ggalign) with:\n\n``` r\n# install.packages(\"remotes\")\nremotes::install_github(\"Yunuuuu/ggalign\")\n```\n\n## Getting Started\n\nThe usage of `ggalign` is simple if you’re familiar with `ggplot2`\nsyntax, the typical workflow includes:\n\n- Initialize the layout using `ggheatmap()` or `ggstack()`.\n- Customize the layout with:\n - `align_group()`: Group layout axis into panel with a group variable.\n - `align_kmeans()`: Group layout axis into panel by kmeans.\n - `align_order()`: Reorder layout observations based on statistical\n weights or by manually specifying the observation index.\n - `align_dendro()`: Reorder or Group layout based on hierarchical\n clustering.\n- Adding plots with `ggalign()` or `ggpanel()`, and then layer\n additional ggplot2 elements such as geoms, stats, or scales.\n\n## Basic example\n\nBelow, we’ll walk through a basic example of using `ggalign` to create a\nheatmap with a `dendrogram`.\n\n``` r\nlibrary(ggalign)\nset.seed(123)\nsmall_mat <- matrix(rnorm(81), nrow = 9)\nrownames(small_mat) <- paste0(\"row\", seq_len(nrow(small_mat)))\ncolnames(small_mat) <- paste0(\"column\", seq_len(ncol(small_mat)))\n\n# initialize the heatmap layout, we can regard it as a normal ggplot object\nggheatmap(small_mat) +\n # we can directly modify geoms, scales and other ggplot2 components\n scale_fill_viridis_c() +\n # add annotation in the top\n hmanno(\"top\") +\n # in the top annotation, we add a dendrogram, and split observations into 3 groups\n align_dendro(aes(color = branch), k = 3) +\n # in the dendrogram we add a point geom\n geom_point(aes(color = branch, y = y)) +\n # change color mapping for the dendrogram\n scale_color_brewer(palette = \"Dark2\")\n```\n\n![](https://yunuuuu.github.io/ggalign/articles/complete-examples_files/figure-html/unnamed-chunk-3-1.png)\n\n## Compare with other ggplot2 heatmap extension\n\n`ggalign` offers advantages over extensions like\n[ggheatmap](https://github.com/XiaoLuo-boy/ggheatmap) by providing full\ncompatibility with `ggplot2`. With `ggalign`, you can:\n\n- Seamlessly integrate ggplot2 `geoms`, `stats`, `scales` et al. into\n your layouts.\n- Align dendrograms even in facetted plots.\n- Easily create complex layouts, including multiple heatmaps arranged\n vertically or horizontally.\n\n## Compare with ComplexHeatmap\n\n### Pros\n\n- Full integration with the `ggplot2` ecosystem.\n- Heatmap annotation axes and legends are automatically generated.\n- Dendrogram can be easily customized and colored.\n- Flexible control over plot size and spacing.\n- Can easily align with other `ggplot2` plots by panel area.\n- Can easily extend for other clustering algorithm, or annotation plot.\n\n### Cons\n\nFewer Built-In Annotations: May require additional coding for specific\nannotations or customization compared to the extensive built-in\nannotation function in\n[ComplexHeatmap](https://github.com/jokergoo/ComplexHeatmap).\n\n## More Complex Examples\n\nHere are some more advanced visualizations using `ggalign`:\n![](https://yunuuuu.github.io/ggalign/articles/more-examples_files/figure-html/unnamed-chunk-3-1.png)\n![](https://yunuuuu.github.io/ggalign/articles/more-examples_files/figure-html/unnamed-chunk-2-1.png)\n\n## Further Documentation\n\n- [Heatmap\n Layout](https://yunuuuu.github.io/ggalign/articles/heatmap-layout.html)\n- [Layout\n Customization](https://yunuuuu.github.io/ggalign/articles/layout-customize.html)\n- [Layout\n Plot](https://yunuuuu.github.io/ggalign/articles/layout-plot.html)\n- [Stack\n Layout](https://yunuuuu.github.io/ggalign/articles/stack-layout.html)\n- [Special Syntax for Layout\n Axis](https://yunuuuu.github.io/ggalign/articles/special-syntax.html)","jobInfo":{"package":"ggalign","version":"0.0.4","parsingStatus":"success","parserVersion":2,"parsedAt":"2024-10-12T15:29:48+0000"}}

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