From 1d6e76ed51135ebbb8d69f8189e270d871a1fe62 Mon Sep 17 00:00:00 2001 From: Yunuuuu Date: Sun, 15 Dec 2024 02:28:29 +0800 Subject: [PATCH] docs update --- README.Rmd | 48 +++++++++++++++++++++++------------------------ README.md | 55 ++++++++++++++++++++++++++---------------------------- 2 files changed, 50 insertions(+), 53 deletions(-) diff --git a/README.Rmd b/README.Rmd index faf94412..49cfc696 100644 --- a/README.Rmd +++ b/README.Rmd @@ -73,27 +73,27 @@ remotes::install_github("Yunuuuu/ggalign") 2. For the full reference documentation, visit: -## Compare with other ggplot2 heatmap extension -`ggalign` offers advantages over extensions like -[ggheatmap](https://github.com/XiaoLuo-boy/ggheatmap) by providing full -compatibility with `ggplot2`. With `ggalign`, you can: - -- Seamlessly integrate ggplot2 `geoms`, `stats`, `scales` et al. into your -layouts. -- Align dendrograms even in facetted plots. -- Easily create complex layouts, including multiple heatmaps arranged vertically - or horizontally. - -## Compare with ComplexHeatmap -### Pros -- Full integration with the `ggplot2` ecosystem. -- Heatmap annotation axes and legends are automatically generated. -- Dendrogram can be easily customized and colored. -- Flexible control over plot size and spacing. -- Can easily align with other `ggplot2` plots by panel area. -- Can easily extend for other clustering algorithm, or annotation plot. - -### Cons -Fewer Built-In Annotations: May require additional coding for specific -annotations or customization compared to the extensive built-in annotation -function in [ComplexHeatmap](https://github.com/jokergoo/ComplexHeatmap). +## Compare with other similar tools + +| | `ggalign` | `ComplexHeatmap` | `marsilea` | `ggheatmap` | +| ----------------------------------- | --------------------------------------------- | ---------------------------------------------------- | ------------------------ | ---------------------------------------------------- | +| **Language** | R | R | Python | R | +| **User Interface** | Declarative | Functional | Declarative | Functional | +| **Plot System** | ggplot2 | grid | seaborn | ggplot2 | +| **Focus** | Composable Visualization | Heatmap | Composable Visualization | Heatmap | +| **Heatmap Layout** | Yes | Yes | Yes | Yes | +| **Marginal Layout** | Yes | No | Yes | No | +| **Stack Layout** | Yes | Yes | Yes | No | +| **Cross Layout** | Yes | No | No | No | +| **Group or Reorder Heatmap** | Yes | Yes | Yes | Yes | +| **Group or Reorder Stack Only** | Yes | No | Yes | No | +| **Separate Group into Slices** | Yes | Yes | Yes | No | +| **Plot Type** | Many, provided by ggplot2 | Many, but limited | Many, but limited | Limited | +| **Legends Creation** | Automatic | Limited automatic, requires manual add | Manual | Automatic | +| **Legends Position** | Anywhere, can be controlled for a single plot | Four sides, can only be placed on one side at a time | ? | Four sides, can only be placed on one side at a time | +| **Dendrogram Position** | Anywhere | Heatmap only | Anywhere | Heatmap only | +| **3D Heatmap** | Yes | Yes | No | No | +| **Oncoplot** | Yes | Yes | Yes | No | +| **Interactive** | No | Yes | No | No | +| **Fully Compatible with ggplot2\*** | Yes | No | No | No | + * It can be considered a benefit, as the ggplot2 ecosystem is highly enriched. diff --git a/README.md b/README.md index 1cc8d6b7..94823432 100644 --- a/README.md +++ b/README.md @@ -66,32 +66,29 @@ remotes::install_github("Yunuuuu/ggalign") 2. For the full reference documentation, visit: -## Compare with other ggplot2 heatmap extension - -`ggalign` offers advantages over extensions like -[ggheatmap](https://github.com/XiaoLuo-boy/ggheatmap) by providing full -compatibility with `ggplot2`. With `ggalign`, you can: - -- Seamlessly integrate ggplot2 `geoms`, `stats`, `scales` et al. into - your layouts. -- Align dendrograms even in facetted plots. -- Easily create complex layouts, including multiple heatmaps arranged - vertically or horizontally. - -## Compare with ComplexHeatmap - -### Pros - -- Full integration with the `ggplot2` ecosystem. -- Heatmap annotation axes and legends are automatically generated. -- Dendrogram can be easily customized and colored. -- Flexible control over plot size and spacing. -- Can easily align with other `ggplot2` plots by panel area. -- Can easily extend for other clustering algorithm, or annotation plot. - -### Cons - -Fewer Built-In Annotations: May require additional coding for specific -annotations or customization compared to the extensive built-in -annotation function in -[ComplexHeatmap](https://github.com/jokergoo/ComplexHeatmap). +## Compare with other similar tools + +| | `ggalign` | `ComplexHeatmap` | `marsilea` | `ggheatmap` | +|-------------------------------------|-----------------------------------------------|------------------------------------------------------|--------------------------|------------------------------------------------------| +| **Language** | R | R | Python | R | +| **User Interface** | Declarative | Functional | Declarative | Functional | +| **Plot System** | ggplot2 | grid | seaborn | ggplot2 | +| **Focus** | Composable Visualization | Heatmap | Composable Visualization | Heatmap | +| **Heatmap Layout** | Yes | Yes | Yes | Yes | +| **Marginal Layout** | Yes | No | Yes | No | +| **Stack Layout** | Yes | Yes | Yes | No | +| **Cross Layout** | Yes | No | No | No | +| **Group or Reorder Heatmap** | Yes | Yes | Yes | Yes | +| **Group or Reorder Stack Only** | Yes | No | Yes | No | +| **Separate Group into Slices** | Yes | Yes | Yes | No | +| **Plot Type** | Many, provided by ggplot2 | Many, but limited | Many, but limited | Limited | +| **Legends Creation** | Automatic | Limited automatic, requires manual add | Manual | Automatic | +| **Legends Position** | Anywhere, can be controlled for a single plot | Four sides, can only be placed on one side at a time | ? | Four sides, can only be placed on one side at a time | +| **Dendrogram Position** | Anywhere | Heatmap only | Anywhere | Heatmap only | +| **3D Heatmap** | Yes | Yes | No | No | +| **Oncoplot** | Yes | Yes | Yes | No | +| **Interactive** | No | Yes | No | No | +| **Fully Compatible with ggplot2\*** | Yes | No | No | No | + +- It can be considered a benefit, as the ggplot2 ecosystem is highly + enriched.