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docs update
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@Yunuuuu
Yunuuuu committed Dec 14, 2024
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48 changes: 24 additions & 24 deletions README.Rmd
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Expand Up @@ -73,27 +73,27 @@ remotes::install_github("Yunuuuu/ggalign")

2. For the full reference documentation, visit: <https://yunuuuu.github.io/ggalign/>

## 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.
55 changes: 26 additions & 29 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -66,32 +66,29 @@ remotes::install_github("Yunuuuu/ggalign")
2. For the full reference documentation, visit:
<https://yunuuuu.github.io/ggalign/>

## 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.

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