Source code for scphylo.datasets._datasets
import scphylo as scp
[docs]def example(is_expression=False):
"""Return an example for sanity checking and playing with scPhylo.
is_expression : :obj:`bool`, optional
Returns the expression dataset instead of the genotype one, by default False
Returns
-------
:class:`anndata.AnnData`
An object that cells are in `.obs` and mutations are in `.var`.
"""
if is_expression:
return scp.io.read(scp.ul.get_file("scphylo.datasets/data/expression.h5ad.gz"))
else:
return scp.io.read(scp.ul.get_file("scphylo.datasets/data/genotype.h5ad.gz"))
def test():
df = scp.io.read(scp.ul.get_file("scphylo.datasets/test/test.tsv"))
return df
[docs]def melanoma20():
"""Mouse Melanoma dataset with 20 sublines.
This dataset was introduced in :cite:`Wolf_2019` and was used in:
* :cite:`PhISCS-BnB` Figure 1.
The size is n_cells × n_muts = 20 × 2367
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
`.layers['solution_fig1']` is the solution presented in Figure 1 of PhISCS-BnB
paper.
"""
adata = scp.io.read(scp.ul.get_file("scphylo.datasets/real/melanoma20.h5ad"))
return adata
[docs]def colorectal1():
"""Human Colorectal Cancer (Patient 1).
This dataset was introduced in :cite:`Leung_2017` and was used in:
* :cite:`B-SCITE` Figure 8a.
* :cite:`SiFit` Figure 6.
* :cite:`SPhyR` Table 1.
* :cite:`SiCloneFit` Figure 3.
The size is n_cells × n_muts = 178 × 16
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
Notes
-----
This dataset includes single cells from two sites of the patient body;
133 single cells from colon as primary tumor site and 45 single cells from liver
as the tumor metastatic site (178 in total). The number of mutations in this
dataset is 16. One can remove the cells in this dataset that carry none of these 16
mutations before feeding it to our network. After removing cells with zero profile,
the number of cells are 40 and 32 from primary and metastatic sites, respectively
(72 in total).
"""
adata = scp.io.read(scp.ul.get_file("scphylo.datasets/real/colorectal1.h5ad"))
return adata
[docs]def colorectal2(readcount=False):
"""Human Colorectal Cancer (Patient 2).
This dataset was introduced in :cite:`Leung_2017` and was used in:
* :cite:`PhISCS` Figure 7.
* :cite:`B-SCITE` Figure 8b.
* :cite:`SiCloneFit` Figure 4.
* :cite:`SCARLET` Figure 4.
The size is n_cells × n_muts = 78 × 25
Parameters
----------
readcount : :obj:`str`
Return the readcount information of the data.
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
- `.layers['solution_fig7a']` is the solution presented in Figure 7a of
PhISCS paper.
- `.layers['solution_fig7b']` is the solution presented in Figure 7b of
PhISCS paper.
- `.uns['params_fig7a']` is parameters used as input to get 'solution_7a'.
- `.uns['params_fig7b']` is parameters used as input to get 'solution_7b'.
- `.var` includes information of the bulk samples.
"""
if readcount:
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/colorectal2.rc.h5ad")
)
else:
adata = scp.io.read(scp.ul.get_file("scphylo.datasets/real/colorectal2.h5ad"))
# FIXME: (86 x 25 in B-SCITE) (182 x 36 SiCloneFit)
# https://github.com/cbg-ethz/infSCITE/blob/master/pat_2.csv
# https://github.com/hzi-bifo/scelestial-paper-materials-devel/tree/master/testing/
return adata
[docs]def colorectal3():
"""Human Colorectal Cancer.
This dataset was introduced in :cite:`Wu_2016` and was used in:
* :cite:`SiFit` Figure 5.
The size is n_cells × n_muts = 48 × 77
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
# adata = scp.io.read(scp.ul.get_file("scphylo.datasets/real/colorectal3.h5ad"))
# TODO: extract
return None
[docs]def acute_lymphocytic_leukemia1():
"""Human Acute Lymphocytic Leukemia dataset (Patient 1).
This dataset was introduced in :cite:`Gawad_2014` and was used in:
* :cite:`B-SCITE` Figure 5.
* :cite:`infSCITE` Figure S16.
The size is n_cells × n_muts = 111 × 20
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/acute_lymphocytic_leukemia1.h5ad")
)
return adata
[docs]def acute_lymphocytic_leukemia2():
"""Human Acute Lymphocytic Leukemia dataset (Patient 2).
This dataset was introduced in :cite:`Gawad_2014` and was used in:
* :cite:`PhISCS` Figure 9.
* :cite:`B-SCITE` in Figure 6.
* :cite:`infSCITE` Figure S17.
* :cite:`Phyolin` Table 2.
The size is n_cells × n_muts = 102 × 16
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
- `.layers['solution_fig9']` is the solution presented in Figure 9 of PhISCS
paper.
- `.uns['params_fig9']` is parameters used as input to get 'solution_fig9'.
- `.var` includes information of the bulk samples.
"""
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/acute_lymphocytic_leukemia2.h5ad")
)
# FIXME: 115 x 16 in B-SCITE?
return adata
[docs]def acute_lymphocytic_leukemia3():
"""Human Acute Lymphocytic Leukemia dataset (Patient 3).
This dataset was introduced in :cite:`Gawad_2014` and was used in:
* :cite:`infSCITE` Figure S18.
* :cite:`SCIPhI` Figure 5.
* :cite:`ScisTree` Figure S3.
The size is n_cells × n_muts = 150 × 49
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/acute_lymphocytic_leukemia3.h5ad")
)
# FIXME: 255 x 49 in SCIPhI and ScisTree?
return adata
[docs]def acute_lymphocytic_leukemia4():
"""Human Acute Lymphocytic Leukemia dataset (Patient 4).
This dataset was introduced in :cite:`Gawad_2014` and was used in:
* :cite:`infSCITE` Figure S19.
* :cite:`gpps` Figure 3.
* :cite:`SASC` Figure 6.
The size is n_cells × n_muts = 143 × 78
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/acute_lymphocytic_leukemia4.h5ad")
)
return adata
[docs]def acute_lymphocytic_leukemia5():
"""Human Acute Lymphocytic Leukemia dataset (Patient 5).
This dataset was introduced in :cite:`Gawad_2014` and was used in:
* :cite:`infSCITE` Figure S20.
* :cite:`SASC` Figure 7.
The size is n_cells × n_muts = 96 × 105
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/acute_lymphocytic_leukemia5.h5ad")
)
return adata
[docs]def acute_lymphocytic_leukemia6():
"""Human Acute Lymphocytic Leukemia dataset (Patient 6).
This dataset was introduced in :cite:`Gawad_2014` and was used in:
* :cite:`infSCITE` Figure S21.
* :cite:`Phyolin` Table 2.
The size is n_cells × n_muts = 146 × 10
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/acute_lymphocytic_leukemia6.h5ad")
)
return adata
[docs]def tnbc():
"""Triple-negative Breast Cancer.
This dataset was introduced in :cite:`Wang_2014` and was used in:
* :cite:`SCIPhI` Figure 4.
* :cite:`B-SCITE` Figure 7.
* :cite:`TRaIT` Figure 6.
The size is n_cells × n_muts = 16 × 20
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
Examples
--------
>>> adata = scp.datasets.tnbc()
>>> df_in = adata.to_df()
"""
adata = scp.io.read(scp.ul.get_file("scphylo.datasets/real/tnbc.h5ad"))
return adata
[docs]def erbc():
"""Oestrogen-receptor-positive (ER+) Breast Cancer.
This dataset was introduced in :cite:`Wang_2014` and was used in:
* :cite:`SCITE` Figure S8 and S9.
* :cite:`infSCITE` Figure S15.
* :cite:`gpps` Figure 1.
The size is n_cells × n_muts = 47 × 40
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
- `.uns['params_scite']` is parameters inferred by SCITE.
Examples
--------
>>> adata = scp.datasets.erbc()
>>> df_in = adata.to_df()
"""
adata = scp.io.read(scp.ul.get_file("scphylo.datasets/real/erbc.h5ad"))
return adata
[docs]def muscle_invasive_bladder():
"""Muscle Invasive Bladder Cancer.
This dataset was introduced in :cite:`Li_2012` and was used in:
* :cite:`OncoNEM` Figure 6B.
The size is n_cells × n_muts = 44 × 443
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
- `.uns['params_onconem']` is parameters inferred by OncoNEM.
Examples
--------
>>> adata = scp.datasets.muscle_invasive_bladder()
>>> df_in = adata.to_df()
"""
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/muscle_invasive_bladder.h5ad")
)
return adata
[docs]def renal_cell_carcinoma():
"""Clear-cell Renal-cell Carcinoma.
This dataset was introduced in :cite:`Xu_2012` and was used in:
* :cite:`SCITE` Figure S6 and S7.
* :cite:`infSCITE` Figure S14.
The size is n_cells × n_muts = 17 × 35
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
- `.uns['params_scite']` is parameters inferred by SCITE.
Examples
--------
>>> adata = scp.datasets.renal_cell_carcinoma()
>>> df_in = adata.to_df()
"""
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/renal_cell_carcinoma.h5ad")
)
return adata
[docs]def myeloproliferative_neoplasms712():
"""JAK2-Negative Myeloproliferative Neoplasm.
This dataset was introduced in :cite:`Hou_2012` and was used in:
* :cite:`OncoNEM` Figure 6D.
The size is n_cells × n_muts = 58 × 712
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
- `.uns['params_onconem']` is parameters inferred by OncoNEM.
"""
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/myeloproliferative_neoplasms712.h5ad")
)
return adata
[docs]def myeloproliferative_neoplasms78():
"""JAK2-Negative Myeloproliferative Neoplasm.
This dataset was introduced in :cite:`Hou_2012` and was used in:
* :cite:`SCITE` Figure S5.
The size is n_cells × n_muts = 58 × 78
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
Notes
-----
The original dataset contains 712 mutations but 78 ones were considered as
non-synonymous mutations from the full data.
"""
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/myeloproliferative_neoplasms78.h5ad")
)
return adata
[docs]def myeloproliferative_neoplasms18():
"""JAK2-Negative Myeloproliferative Neoplasm.
This dataset was introduced in :cite:`Hou_2012` and was used in:
* :cite:`SCITE` Figure S2, S3 and S4.
* :cite:`Kim_2014` Figure 1.
* :cite:`infSCITE` Figure S13.
* :cite:`gpps` Figure 2.
The size is n_cells × n_muts = 58 × 18
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
- `.uns['params_scite']` is parameters inferred by SCITE.
Notes
-----
The original dataset contains 712 mutations but 18 ones were considered as
cancer related mutations from the full data.
"""
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/myeloproliferative_neoplasms18.h5ad")
)
return adata
[docs]def high_grade_serous_ovarian_cancer1():
"""High Grade Serous Ovarian Cancer (Patient 2).
This dataset was introduced in :cite:`McPherson_2016` and was used in:
* :cite:`infSCITE` Figure S22.
The size is n_cells × n_muts = 588 × 37
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
# adata = scp.io.read(
# scp.ul.get_file(
# "scphylo.datasets/real/high_grade_serous_ovarian_cancer1.h5ad"
# )
# )
# TODO: extract
return None
[docs]def high_grade_serous_ovarian_cancer2():
"""High Grade Serous Ovarian Cancer (Patient 3).
This dataset was introduced in :cite:`McPherson_2016` and was used in:
* :cite:`infSCITE` Figure S23.
The size is n_cells × n_muts = 672 × 60
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
# adata = scp.io.read(
# scp.ul.get_file(
# "scphylo.datasets/real/high_grade_serous_ovarian_cancer2.h5ad"
# )
# )
# TODO: extract
return None
[docs]def high_grade_serous_ovarian_cancer3():
"""High Grade Serous Ovarian Cancer (Patient 9).
This dataset was introduced in :cite:`McPherson_2016` and was used in:
* :cite:`infSCITE` Figure S24.
* :cite:`scVILP` Figure 5.
* :cite:`SCIPhI` Figure S10.
The size is n_cells × n_muts = 420 × 37
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
# adata = scp.io.read(
# scp.ul.get_file(
# "scphylo.datasets/real/high_grade_serous_ovarian_cancer3.h5ad"
# )
# )
# TODO: extract
# FIXME: 370 x 43 in scVILP and SCIPhI?
return None
[docs]def high_grade_serous_ovarian_cancer_3celllines():
"""High Grade Serous Ovarian Cancer (3 cell lines).
This dataset was introduced in :cite:`Laks_2019`
and preprocessed in :cite:`McPherson_2019`.
The phylogeny is presented in Figure 3H.
The size is n_cells × n_muts = 891 × 13666
Note that 402 mutations were deleted during evolution
in the inferred tree by original study So, here they were filtered out
(meaning they are 14068 mutations in total in the original study).
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy
(it is obtained based on the number of mutant/total reads).
- `.obs['clone_id']` is the clone id to which the cell is assigned in
Figure 3H.
- `.obs['group_color']` is unique colors for each 'clone_id'.
- `.obs['cell_name']` is a new name for each cell based on the
'group_color'.
- `.layers['mutant']` is the number of mutant reads at each locus in each
cell.
- `.layers['total']` is the total number of reads at each locus in each
cell.
- `.layers['ground']` is the solution inferred in Figure 3H of the original
paper.
- `.uns['params_ground']` is parameters inferred by comparing ground and
noisy matrices.
- `.var` includes information of the bulk samples.
Examples
--------
>>> sc = scp.datasets.high_grade_serous_ovarian_cancer_3celllines()
>>> print(sc)
AnnData object with n_obs × n_vars = 891 × 13666
obs: 'clone_id', 'group_color', 'cell_name'
uns: 'params_ground'
layers: 'ground', 'mutant', 'total'
"""
adata = scp.io.read(scp.ul.get_file("scphylo.datasets/real/ovarian.h5ad.gz"))
return adata
def oligodendroglioma_idh_mutated_tumor():
"""Oligodendroglioma IDH-mutated tumor.
This dataset was introduced in :cite:`Tirosh_2016` and was used in:
* :cite:`SASC` Figure 5.
The size is n_cells × n_muts = 579 × 77
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
adata = scp.io.read(
scp.ul.get_file(
"scphylo.datasets/real/oligodendroglioma_idh_mutated_tumor.h5ad"
)
)
return adata
def acute_lymphocytic_leukemia_many():
"""Human Acute Lymphocytic Leukemia datasets.
This dataset was introduced in :cite:`Morita_2020` and was used in:
* :cite:`Phyolin` Figure 3 and Table 1.
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
# TODO: extract all
return None
def isogenic_fibroblast_cell_line():
"""Isogenic Fibroblast cell line dataset.
This dataset was introduced in :cite:`Leung_2015` and was used in:
* :cite:`SCIPhI` Figure S9.
The size is n_cells × n_muts = 19 × ?
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
# TODO: extract
return None
[docs]def acute_myeloid_leukemia1():
"""Human Acute Myeloid Leukemia dataset (Patient 1).
This dataset was introduced in :cite:`Velten_2021` and was used in:
The size is n_cells × n_muts = 1430 × 15
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/acute_myeloid_leukemia1.h5ad")
)
return adata
[docs]def acute_myeloid_leukemia2():
"""Human Acute Myeloid Leukemia dataset (Patient 2).
This dataset was introduced in :cite:`Velten_2021` and was used in:
The size is n_cells × n_muts = 1066 × 21
Returns
-------
:class:`anndata.AnnData`
An anndata in which `.X` is the input noisy.
"""
adata = scp.io.read(
scp.ul.get_file("scphylo.datasets/real/acute_myeloid_leukemia2.h5ad")
)
return adata