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docs update
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@Yunuuuu
Yunuuuu committed Jan 13, 2025
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30 changes: 15 additions & 15 deletions README.Rmd
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Expand Up @@ -187,21 +187,21 @@ remotes::install_github("Yunuuuu/ggalign")

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

| Specification | `ggalign` | `ComplexHeatmap` | `marsilea` | `ggtree` |
| -------------------------------------------- | ----------------------------------------------------- | ------------------------------------------------------------------------- | ----------------- | ----------------------------------- |
| **Data input** | Various, and can be easily extended | fixed | fixed | Various, and can be easily extended |
| **Plot Type** | Wide variety, provided by ggplot2 | Many, but limited | Many, but limited | Limited Geometric layers support |
| **Reorder observations** | ✅ | Heatmap Only (Cannot be used in Stack Layout) | ✅ | ✅ |
| **Group observations into different panels** | ✅ | Heatmap Only (Cannot be used in Stack Layout) | ✅ | ❌ |
| **Clustering algorithm** | Kmeans,Hierarchical Clustering and arbitary algorithm | Kmeans,Hierarchical Clustering, but can provide clustering group directly | ❌ | ❌ |
| **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 | ? | Anywhere |
| **Scientific Color Palettes** | Many | Limited | Limited | Many |
| **Dendrogram** | Tree from Both `hclust` or `ape` | `hclust` only (Cannot be used in Stack Layout) | `hclust` only | Tree from Both `hclust` or `ape` |
| **Tanglegram** | ✅ | ❌ | ❌ | ❌ |
| **3D Heatmap** | ✅ | ✅ | ❌ | ❌ |
| **Oncoplot** | ✅ | ✅ | ✅ | ❌ |
| **UpSet plot** | ✅ | ✅ | ✅ | ❌ |
| Specification | `ggalign` | `marsilea` | `ComplexHeatmap` | `ggtree` |
| -------------------------------------------- | ----------------------------------------------------- | ----------------- | ------------------------------------------------------------------------- | ----------------------------------- |
| **Data input** | Various, and can be easily extended | fixed | fixed | Various, and can be easily extended |
| **Plot Type** | Wide variety, provided by ggplot2 | Many, but limited | Many, but limited | Limited Geometric layers support |
| **Reorder observations** | ✅ | ✅ | Heatmap Only (Cannot be used in Stack Layout) | ✅ |
| **Group observations into different panels** | ✅ | ✅ | Heatmap Only (Cannot be used in Stack Layout) | ❌ |
| **Clustering algorithm** | Kmeans,Hierarchical Clustering and arbitary algorithm | ❌ | Kmeans,Hierarchical Clustering, but can provide clustering group directly | ❌ |
| **Legends Creation** | Automatic | Manual | Limited automatic, requires manual add | Automatic |
| **Legends Position** | Anywhere, can be controlled for a single plot | ? | Four sides, can only be placed on one side at a time | Anywhere |
| **Scientific Color Palettes** | Many | Limited | Limited | Many |
| **Dendrogram** | Tree from Both `hclust` or `ape` | `hclust` only | `hclust` only (Cannot be used in Stack Layout) | Tree from Both `hclust` or `ape` |
| **Tanglegram** | ✅ | ❌ | ❌ | ❌ |
| **3D Heatmap** | ✅ | ❌ | ✅ | ❌ |
| **Oncoplot** | ✅ | ✅ | ✅ | ❌ |
| **UpSet plot** | ✅ | ✅ | ✅ | ❌ |

## Acknowledgements
I would like to express my sincere gratitude to the contributors of the
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30 changes: 15 additions & 15 deletions README.md
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Expand Up @@ -334,21 +334,21 @@ Limited Geometric layers support

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

| Specification | `ggalign` | `ComplexHeatmap` | `marsilea` | `ggtree` |
|----------------------------------------------|-------------------------------------------------------|---------------------------------------------------------------------------|-------------------|-------------------------------------|
| **Data input** | Various, and can be easily extended | fixed | fixed | Various, and can be easily extended |
| **Plot Type** | Wide variety, provided by ggplot2 | Many, but limited | Many, but limited | Limited Geometric layers support |
| **Reorder observations** | ✅ | Heatmap Only (Cannot be used in Stack Layout) | ✅ | ✅ |
| **Group observations into different panels** | ✅ | Heatmap Only (Cannot be used in Stack Layout) | ✅ | ❌ |
| **Clustering algorithm** | Kmeans,Hierarchical Clustering and arbitary algorithm | Kmeans,Hierarchical Clustering, but can provide clustering group directly | ❌ | ❌ |
| **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 | ? | Anywhere |
| **Scientific Color Palettes** | Many | Limited | Limited | Many |
| **Dendrogram** | Tree from Both `hclust` or `ape` | `hclust` only (Cannot be used in Stack Layout) | `hclust` only | Tree from Both `hclust` or `ape` |
| **Tanglegram** | ✅ | ❌ | ❌ | ❌ |
| **3D Heatmap** | ✅ | ✅ | ❌ | ❌ |
| **Oncoplot** | ✅ | ✅ | ✅ | ❌ |
| **UpSet plot** | ✅ | ✅ | ✅ | ❌ |
| Specification | `ggalign` | `marsilea` | `ComplexHeatmap` | `ggtree` |
|----------------------------------------------|-------------------------------------------------------|-------------------|---------------------------------------------------------------------------|-------------------------------------|
| **Data input** | Various, and can be easily extended | fixed | fixed | Various, and can be easily extended |
| **Plot Type** | Wide variety, provided by ggplot2 | Many, but limited | Many, but limited | Limited Geometric layers support |
| **Reorder observations** | ✅ | ✅ | Heatmap Only (Cannot be used in Stack Layout) | ✅ |
| **Group observations into different panels** | ✅ | ✅ | Heatmap Only (Cannot be used in Stack Layout) | ❌ |
| **Clustering algorithm** | Kmeans,Hierarchical Clustering and arbitary algorithm | ❌ | Kmeans,Hierarchical Clustering, but can provide clustering group directly | ❌ |
| **Legends Creation** | Automatic | Manual | Limited automatic, requires manual add | Automatic |
| **Legends Position** | Anywhere, can be controlled for a single plot | ? | Four sides, can only be placed on one side at a time | Anywhere |
| **Scientific Color Palettes** | Many | Limited | Limited | Many |
| **Dendrogram** | Tree from Both `hclust` or `ape` | `hclust` only | `hclust` only (Cannot be used in Stack Layout) | Tree from Both `hclust` or `ape` |
| **Tanglegram** | ✅ | ❌ | ❌ | ❌ |
| **3D Heatmap** | ✅ | ❌ | ✅ | ❌ |
| **Oncoplot** | ✅ | ✅ | ✅ | ❌ |
| **UpSet plot** | ✅ | ✅ | ✅ | ❌ |

## Acknowledgements

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