You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: README.md
+37-14Lines changed: 37 additions & 14 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -8,7 +8,8 @@
8
8
9
9
The **DicePlot** package allows you to create visualizations (dice plots) for datasets with more than two categorical variables and additional continuous variables. This tool is particularly useful for exploring complex categorical data and their relationships with continuous variables.
10
10
11
-
## Installation
11
+
<details>
12
+
<summary><h2>Installation</h2></summary>
12
13
13
14
To install the **DicePlot** package, follow these steps:
14
15
@@ -67,8 +68,10 @@ After installation, load the `DicePlot` package into your R session:
Here is a simple example of how to use the `DicePlot v0.1.2` package.
74
77
For more examples, check the tests/ folder.
@@ -169,8 +172,10 @@ print(p)
169
172
170
173
### Output
171
174

175
+
</details>
172
176
173
-
## Domino Plot Tutorial
177
+
<details>
178
+
<summary><h2>Domino Plot Tutorial</h2></summary>
174
179
175
180
### Introduction to Domino Plots
176
181
@@ -359,9 +364,11 @@ In a domino plot:
359
364
- x-axis: Typically genes
360
365
- y-axis: Typically cell types
361
366
- Facets (if used): Can represent different conditions or contrasts
367
+
</details>
362
368
369
+
<details>
370
+
<summary><h2>geom_dice_sf Tutorial</h2></summary>
363
371
364
-
## geom_dice_sf Tutorial
365
372
### Prerequisites
366
373
This tutorial has prerquisties which are not defaults in the diceplot package itself.
367
374
Before proceeding, install the required R packages:
@@ -484,35 +491,46 @@ final_plot
484
491
```
485
492
### Output
486
493

494
+
</details>
487
495
488
-
489
-
## Use DicePlot in Python
496
+
<details>
497
+
<summary><h2>Use DicePlot in Python</h2></summary>
490
498
491
499
For using dice plots in Python, please refer to [pyDicePlot](https://github.com/maflot/pyDicePlot/tree/main)
500
+
</details>
492
501
493
-
## Documentation
502
+
<details>
503
+
<summary><h2>Documentation</h2></summary>
494
504
495
505
For full documentation and additional examples, please refer to the [documentation](https://dice-and-domino-plot.readthedocs.io/en/latest/index.html#)
506
+
</details>
496
507
497
-
## Features
508
+
<details>
509
+
<summary><h2>Features</h2></summary>
498
510
499
511
-**Visualize Complex Data:** Easily create plots for datasets with multiple categorical variables.
500
512
-**Customization:** Customize plots with titles, labels, and themes.
501
513
-**Integration with ggplot2:** Leverages the power of `ggplot2` for advanced plotting capabilities.
514
+
</details>
502
515
503
-
## Contributing
516
+
<details>
517
+
<summary><h2>Contributing</h2></summary>
504
518
505
519
We welcome contributions from the community! If you'd like to contribute:
506
520
507
521
1. Fork the repository on GitHub.
508
522
2. Create a new branch for your feature or bug fix.
509
523
3. Submit a pull request with a detailed description of your changes.
524
+
</details>
510
525
511
-
## Contact
526
+
<details>
527
+
<summary><h2>Contact</h2></summary>
512
528
513
529
If you have any questions, suggestions, or issues, please open an issue on GitHub.
530
+
</details>
514
531
515
-
## Change Log v0.1.6
532
+
<details>
533
+
<summary><h2>Change Log v0.1.6</h2></summary>
516
534
517
535
- Update the examples to real world data
518
536
- move example files out of test to example
@@ -524,8 +542,10 @@ If you have any questions, suggestions, or issues, please open an issue on GitHu
524
542
### domino_plot function
525
543
- Add proper legend to the plot, remove intermediate plot
526
544
- Default logfc crop to NULL
545
+
</details>
527
546
528
-
## Citation
547
+
<details>
548
+
<summary><h2>Citation</h2></summary>
529
549
530
550
If you use this code or the R and Python packages for your own work, please cite diceplot as:
531
551
@@ -541,9 +561,12 @@ BibTeX entry:
541
561
doi = {https://doi.org/10.48550/arXiv.2410.23897}
542
562
}
543
563
```
564
+
</details>
544
565
545
-
## References
566
+
<details>
567
+
<summary><h2>References</h2></summary>
546
568
547
569
[1] Flotho, M., Flotho, P., Keller, A. (2024). Diceplot: A package for high dimensional categorical data visualization. *arXiv preprint*. https://doi.org/10.48550/arXiv.2410.23897
548
570
549
-
[2] Flotho, M., Amand, J., Hirsch, P., Grandke, F., Wyss-Coray, T., Keller, A., Kern, F. (2023). ZEBRA: a hierarchically integrated gene expression atlas of the murine and human brain at single-cell resolution. *Nucleic Acids Research*, 52(D1), D1089-D1096. https://doi.org/10.1093/nar/gkad990
571
+
[2] Flotho, M., Amand, J., Hirsch, P., Grandke, F., Wyss-Coray, T., Keller, A., Kern, F. (2023). ZEBRA: a hierarchically integrated gene expression atlas of the murine and human brain at single-cell resolution. *Nucleic Acids Research*, 52(D1), D1089-D1096. https://doi.org/10.1093/nar/gkad990
0 commit comments