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docs update
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@Yunuuuu
Yunuuuu committed Jan 21, 2025
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30 changes: 13 additions & 17 deletions README.Rmd
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Expand Up @@ -182,23 +182,19 @@ remotes::install_github("Yunuuuu/ggalign")
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```

-------------------------------------------------------------------------------

| Specification | `ggalign` | `marsilea` | `aplot` | `ComplexHeatmap` |
| -------------------------------------------- | ----------------------------------------------------- | ----------------- | ----------------------------------- | ----------------------------------------------------- |
| **Data input** | Various, and can be easily extended | fixed | Various, and can be easily extended | fixed |
| **Plot Type** | Wide variety, provided by ggplot2 | Many, but limited | ✅ | Many, but limited |
| **Reorder observations** | ✅ | ✅ | ✅ | Heatmap Only |
| **Group observations into different panels** | ✅ | ✅ | ❌ | Heatmap Only |
| **Clustering algorithm** | Kmeans,Hierarchical Clustering and arbitary algorithm | ❌ | ❌ | Kmeans,Hierarchical Clustering and arbitary algorithm |
| **Legends Creation** | Automatic | Manual | Automatic | Limited automatic, requires manual add |
| **Legends Position** | Anywhere, can be controlled for a single plot | ? | Anywhere | Four sides, can only be placed on one side at a time |
| **Scientific Color Palettes** | Many | Limited | Many | Limited |
| **Dendrogram** | Tree from Both `hclust` or `ape` | `hclust` only | ❌ | `hclust` only |
| **Tanglegram** | ✅ | ❌ | ❌ | ❌ |
| **3D Heatmap** | ✅ | ❌ | ❌ | ✅ |
| **Oncoplot** | ✅ | ✅ | ❌ | ✅ |
| **UpSet plot** | ✅ | ✅ | ❌ | ✅ |
## Comparison of specifications with other similar tools
| Specification | `ggalign` | `marsilea` | `aplot` | `ComplexHeatmap` |
| -------------------------------------------- | ----------------------------------------------------- | ------------- | -------------------------------- | ----------------------------------------------------- |
| **Reorder observations** | ✅ | ✅ | ❌ | Heatmap Only |
| **Group observations into different panels** | ✅ | ✅ | ❌ | Heatmap Only |
| **Clustering algorithm** | Kmeans,Hierarchical Clustering and arbitary algorithm | ❌ | ❌ | Kmeans,Hierarchical Clustering and arbitary algorithm |
| **Legends Creation** | Automatic | Manual | Automatic | Limited automatic, requires manual add |
| **Legends Position** | Anywhere, can be controlled for a single plot | ? | Anywhere | Four sides, can only be placed on one side at a time |
| **Dendrogram** | Tree from Both `hclust` or `ape` | `hclust` only | Tree from Both `hclust` or `ape` | `hclust` only |
| **Tanglegram** | ✅ | ❌ | ❌ | ❌ |
| **3D Heatmap** | ✅ | ❌ | ❌ | ✅ |
| **Oncoplot** | ✅ | ✅ | ✅ | ✅ |
| **UpSet plot** | ✅ | ✅ | ❌ | ✅ |

## Acknowledgements
I would like to express my sincere gratitude to the contributors of the
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31 changes: 14 additions & 17 deletions README.md
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Expand Up @@ -175,23 +175,20 @@ remotes::install_github("Yunuuuu/ggalign")
</tr>
</tbody></table>

------------------------------------------------------------------------

| Specification | `ggalign` | `marsilea` | `aplot` | `ComplexHeatmap` |
|----------------------------------------------|-------------------------------------------------------|-------------------|-------------------------------------|-------------------------------------------------------|
| **Data input** | Various, and can be easily extended | fixed | Various, and can be easily extended | fixed |
| **Plot Type** | Wide variety, provided by ggplot2 | Many, but limited | ✅ | Many, but limited |
| **Reorder observations** | ✅ | ✅ | ✅ | Heatmap Only |
| **Group observations into different panels** | ✅ | ✅ | ❌ | Heatmap Only |
| **Clustering algorithm** | Kmeans,Hierarchical Clustering and arbitary algorithm | ❌ | ❌ | Kmeans,Hierarchical Clustering and arbitary algorithm |
| **Legends Creation** | Automatic | Manual | Automatic | Limited automatic, requires manual add |
| **Legends Position** | Anywhere, can be controlled for a single plot | ? | Anywhere | Four sides, can only be placed on one side at a time |
| **Scientific Color Palettes** | Many | Limited | Many | Limited |
| **Dendrogram** | Tree from Both `hclust` or `ape` | `hclust` only | ❌ | `hclust` only |
| **Tanglegram** | ✅ | ❌ | ❌ | ❌ |
| **3D Heatmap** | ✅ | ❌ | ❌ | ✅ |
| **Oncoplot** | ✅ | ✅ | ❌ | ✅ |
| **UpSet plot** | ✅ | ✅ | ❌ | ✅ |
## Comparison of specifications with other similar tools

| Specification | `ggalign` | `marsilea` | `aplot` | `ComplexHeatmap` |
|----------------------------------------------|-------------------------------------------------------|---------------|----------------------------------|-------------------------------------------------------|
| **Reorder observations** | ✅ | ✅ | ❌ | Heatmap Only |
| **Group observations into different panels** | ✅ | ✅ | ❌ | Heatmap Only |
| **Clustering algorithm** | Kmeans,Hierarchical Clustering and arbitary algorithm | ❌ | ❌ | Kmeans,Hierarchical Clustering and arbitary algorithm |
| **Legends Creation** | Automatic | Manual | Automatic | Limited automatic, requires manual add |
| **Legends Position** | Anywhere, can be controlled for a single plot | ? | Anywhere | Four sides, can only be placed on one side at a time |
| **Dendrogram** | Tree from Both `hclust` or `ape` | `hclust` only | Tree from Both `hclust` or `ape` | `hclust` only |
| **Tanglegram** | ✅ | ❌ | ❌ | ❌ |
| **3D Heatmap** | ✅ | ❌ | ❌ | ✅ |
| **Oncoplot** | ✅ | ✅ | ✅ | ✅ |
| **UpSet plot** | ✅ | ✅ | ❌ | ✅ |

## Acknowledgements

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