From 28b36ad25d65043d87a95e91303e148ba8670cfd Mon Sep 17 00:00:00 2001 From: Kevin Wang Date: Thu, 16 Nov 2023 19:26:11 -0600 Subject: [PATCH 1/3] Update documentation and references. Our Cytomulate paper is recently published on Genome Biology. Hooray! --- README.md | 24 ++++++++++++++---------- docs/source/index.rst | 4 ++-- docs/source/references.rst | 26 +++++++++++++++----------- 3 files changed, 31 insertions(+), 23 deletions(-) diff --git a/README.md b/README.md index 34e2995..98f2eb0 100644 --- a/README.md +++ b/README.md @@ -180,19 +180,23 @@ Update is strongly recommended. ## References -If you used ``PyCytoData`` in your research or with ``Cytomulate`` as part of the pipeline, please cite [our paper](https://doi.org/10.1101/2022.06.14.496200) here: +If you used ``PyCytoData`` in your research or with ``Cytomulate`` as part of the pipeline, please cite [our paper](https://doi.org/10.1186/s13059-023-03099-1) here: ``` -@article {Yang2022.06.14.496200, +Yang, Y., Wang, K., Lu, Z. et al. Cytomulate: accurate and efficient simulation of CyTOF data. Genome Biol 24, 262 (2023). https://doi.org/10.1186/s13059-023-03099-1 +``` + +or with our BibTex: + +``` +@article {Yang2023, author = {Yang, Yuqiu and Wang, Kaiwen and Lu, Zeyu and Wang, Tao and Wang, Xinlei}, - title = {Cytomulate: Accurate and Efficient Simulation of CyTOF data}, - elocation-id = {2022.06.14.496200}, - year = {2022}, - doi = {10.1101/2022.06.14.496200}, - publisher = {Cold Spring Harbor Laboratory}, - URL = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200}, - eprint = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200.full.pdf}, - journal = {bioRxiv} + title = {Cytomulate: accurate and efficient simulation of CyTOF data}, + journal={Genome biology}, + volume={24}, + number={262}, + year={2023}, + publisher={Springer} } ``` diff --git a/docs/source/index.rst b/docs/source/index.rst index 3bd75b5..99e4591 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -65,7 +65,7 @@ tutorials below! Enjoy your journey working with CyTOF datasets! :hidden: references - Our Paper (Cytomulate) + Our Paper (Cytomulate) CyTOF DR Review (CytofDR) Dr. Xinlei (Shery) Wang Dr. Tao Wang @@ -80,7 +80,7 @@ Resources For more resources on our labs, collaborators, and related projects, please visit the following: - * `Our Paper (Cytomulate) `_ + * `Our Paper (Cytomulate) `_ * `CyTOF DR Review Paper (CytofDR) `_ * `Dr. Xinlei (Shery) Wang faculty page `_ * `Dr. Tao Wang Lab `_ diff --git a/docs/source/references.rst b/docs/source/references.rst index e861dd6..728b7f7 100644 --- a/docs/source/references.rst +++ b/docs/source/references.rst @@ -2,21 +2,25 @@ References ################ -If you used ``PyCytoData`` as part of your research or used ``Cytomulate`` with this package, `our paper `_ +If you used ``PyCytoData`` as part of your research or used ``Cytomulate`` with this package, `our paper `_ can be cited here: +.. code-block:: + + Yang, Y., Wang, K., Lu, Z. et al. Cytomulate: accurate and efficient simulation of CyTOF data. Genome Biol 24, 262 (2023). https://doi.org/10.1186/s13059-023-03099-1 + +or + .. code-block:: - @article {Yang2022.06.14.496200, + @article {Yang2023, author = {Yang, Yuqiu and Wang, Kaiwen and Lu, Zeyu and Wang, Tao and Wang, Xinlei}, - title = {Cytomulate: Accurate and Efficient Simulation of CyTOF data}, - elocation-id = {2022.06.14.496200}, - year = {2022}, - doi = {10.1101/2022.06.14.496200}, - publisher = {Cold Spring Harbor Laboratory}, - URL = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200}, - eprint = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200.full.pdf}, - journal = {bioRxiv} + title = {Cytomulate: accurate and efficient simulation of CyTOF data}, + journal={Genome biology}, + volume={24}, + number={262}, + year={2023}, + publisher={Springer} } @@ -55,7 +59,7 @@ Benchmark Datasets ******************** If you use the builtin datasets (``levine13``, ``levine32``, ``samusik``), you can cite the following papers -along with ``HDCytoData``, which hosts these datasets. +along with ``HDCytoData``, which serves as the inspiration for this package. - Weber, L. M., & Soneson, C. (2019). HDCytoData: collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats. F1000Research, 8. - Levine et al. (2015). Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell, 162, pp. 184-197. From 24cdc255de4c929351a1abab23b04d7f27c1c5b8 Mon Sep 17 00:00:00 2001 From: Kevin Wang Date: Thu, 16 Nov 2023 19:28:03 -0600 Subject: [PATCH 2/3] [Doc] Update docstrings Docstrings are improved for the `__getitem__` magic method and the `preprocess` method for the `PyCytoData` class. --- PyCytoData/data.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/PyCytoData/data.py b/PyCytoData/data.py index f9d537f..6eacf9e 100644 --- a/PyCytoData/data.py +++ b/PyCytoData/data.py @@ -189,6 +189,7 @@ def preprocess(self, 3. Gate for intact cells. 4. Gate for live cells. 5. Gate for anomalies using center, offset, and residual channels. + 6. Bead normalization. :param gate_debris_removal: Whether to gate to remove debris, defaults to True. :type gate_debris_removal: bool @@ -519,11 +520,11 @@ def __getitem__(self, items: Union[slice, List[int], np.ndarray, Tuple[Union[sli A few deviations from the numpy notations: - 1. Integer indices are currently not supported. This is because indexing by integer - returns a 1-d array instead of a 2-d array, which can possibly cause confusion. - 2. Indexing by two lists or arrays with different lengths are supported. They are - treated to index rows and columns, such as ``exprs[[0,1,2], [3,4]]`` is perfectly - valid to index the first 3 cells with the fourth and fifth channel. + 1. Integer indices are currently not supported. This is because indexing by + integer returns a 1-d array instead of a 2-d array, which can possibly cause confusion. + 2. Indexing by two lists or arrays with different lengths are supported. + They are treated to index rows and columns, such as ``exprs[[0,1,2], [3,4]]`` is + perfectly valid to index the first 3 cells with the fourth and fifth channel. .. tip:: From e8eef37831296f3e0c8097b39ce02000294f656f Mon Sep 17 00:00:00 2001 From: Kevin Wang Date: Thu, 16 Nov 2023 19:30:54 -0600 Subject: [PATCH 3/3] [Doc] Fix a quick typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 98f2eb0..9441b96 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ # PyCytoData > An elegant data analysis tool for CyTOF. -This package is an all-in-one CyTOF data analysis package for your experiments. From loading datasets to DR and evaluation, you have a consistent interface and readable code every step along the way. There is also support for some of ``HDCytoData``'s benchmark datasets as originally implemented in R by Weber & Soneson (2019) in [this repository](https://github.com/lmweber/HDCytoData). Why wait? Start your PyCytoData journal right here, right now! +This package is an all-in-one CyTOF data analysis package for your experiments. From loading datasets to DR and evaluation, you have a consistent interface and readable code every step along the way. There is also support for some of ``HDCytoData``'s benchmark datasets as originally implemented in R by Weber & Soneson (2019) in [this repository](https://github.com/lmweber/HDCytoData). Why wait? Start your PyCytoData journey right here, right now! ## Installation