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docs update
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@Yunuuuu
Yunuuuu committed Jan 14, 2025
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48 changes: 24 additions & 24 deletions README.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ remotes::install_github("Yunuuuu/ggalign")
<th> <code>ggalign</code> </th>
<th> <code>marsilea</code> </th>
<th> <code>ComplexHeatmap</code> </th>
<th> <code>ggtree</code> </th>
<th> <code>ggtree+aplot</code> </th>
</tr></thead>
<tbody>
<tr>
Expand Down Expand Up @@ -113,28 +113,28 @@ remotes::install_github("Yunuuuu/ggalign")
<td>tree Data</td>
</tr>
<tr>
<td colspan="2"> <strong>Stack Layout</strong> </td>
<td colspan="2"> <strong>StackLayout</strong> </td>
<td>✅</td>
<td>✅</td>
<td>✅</td>
<td>✅</td>
<td>❌</td>
</tr>
<tr>
<td colspan="2"> <strong>Quad Layout</strong> </td>
<td colspan="2"> <strong>QuadLayout</strong> </td>
<td>✅</td>
<td>✅</td>
<td>Heatmap Only (discrete variables)</td>
<td>❌</td>
<td>Cannot arrange multiple QuadLayouts</td>
</tr>
<tr>
<td colspan="2"> <strong>Circle Layout</strong> </td>
<td>✅</td>
<td colspan="2"> <strong>CircleLayout</strong> </td>
<td>Arc with angle >= 90</td>
<td>❌</td>
<td>❌</td>
<td>✅</td>
</tr>
<tr>
<td colspan="2"> <strong>Cross Layout</strong> </td>
<td colspan="2"> <strong>CrossLayout</strong> </td>
<td>✅</td>
<td>❌</td>
<td>❌</td>
Expand Down Expand Up @@ -181,27 +181,27 @@ remotes::install_github("Yunuuuu/ggalign")
<td>✅</td>
<td>❌</td>
<td>❌</td>
<td>Limited Geometric layers support</td>
<td>Limited Geometric layers support in <code>CircleLayout</code></td>
</tr>
</tbody></table>

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

| 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** | ✅ | ✅ | ✅ | ❌ |
| Specification | `ggalign` | `marsilea` | `ComplexHeatmap` | `ggtree+aplot` |
| -------------------------------------------- | ----------------------------------------------------- | ----------------- | ------------------------------------------------------------------------- | -------------------------------------------------- |
| **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 in `CircleLayout` |
| **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 StackLayout) | 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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48 changes: 24 additions & 24 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@ remotes::install_github("Yunuuuu/ggalign")
<code>ComplexHeatmap</code>
</th>
<th>
<code>ggtree</code>
<code>ggtree+aplot</code>
</th>
</tr>
</thead>
Expand Down Expand Up @@ -158,7 +158,7 @@ tree Data
</tr>
<tr>
<td colspan="2">
<strong>Stack Layout</strong>
<strong>StackLayout</strong>
</td>
<td>
✅
Expand All @@ -170,12 +170,12 @@ tree Data
✅
</td>
<td>
❌
✅
</td>
</tr>
<tr>
<td colspan="2">
<strong>Quad Layout</strong>
<strong>QuadLayout</strong>
</td>
<td>
✅
Expand All @@ -187,15 +187,15 @@ tree Data
Heatmap Only (discrete variables)
</td>
<td>
❌
Cannot arrange multiple QuadLayouts
</td>
</tr>
<tr>
<td colspan="2">
<strong>Circle Layout</strong>
<strong>CircleLayout</strong>
</td>
<td>
✅
Arc with angle \>= 90
</td>
<td>
❌
Expand All @@ -209,7 +209,7 @@ Heatmap Only (discrete variables)
</tr>
<tr>
<td colspan="2">
<strong>Cross Layout</strong>
<strong>CrossLayout</strong>
</td>
<td>
✅
Expand Down Expand Up @@ -326,29 +326,29 @@ Easy for ggplot2 users
❌
</td>
<td>
Limited Geometric layers support
Limited Geometric layers support in <code>CircleLayout</code>
</td>
</tr>
</tbody>
</table>

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

| 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** | ✅ | ✅ | ✅ | ❌ |
| Specification | `ggalign` | `marsilea` | `ComplexHeatmap` | `ggtree+aplot` |
|----------------------------------------------|-------------------------------------------------------|-------------------|---------------------------------------------------------------------------|----------------------------------------------------|
| **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 in `CircleLayout` |
| **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 StackLayout) | Tree from Both `hclust` or `ape` |
| **Tanglegram** | ✅ | ❌ | ❌ | ❌ |
| **3D Heatmap** | ✅ | ❌ | ✅ | ❌ |
| **Oncoplot** | ✅ | ✅ | ✅ | ❌ |
| **UpSet plot** | ✅ | ✅ | ✅ | ❌ |

## Acknowledgements

Expand Down

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