diff --git a/README.Rmd b/README.Rmd index 909dd02d..f29e4cfd 100644 --- a/README.Rmd +++ b/README.Rmd @@ -182,23 +182,19 @@ remotes::install_github("Yunuuuu/ggalign") ``` -------------------------------------------------------------------------------- - -| 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 diff --git a/README.md b/README.md index 7ce6eb95..fc5a6afe 100644 --- a/README.md +++ b/README.md @@ -175,23 +175,20 @@ remotes::install_github("Yunuuuu/ggalign") ------------------------------------------------------------------------- - -| 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