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Update tutorial with example_data.
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@emunozdc
emunozdc committed Jun 25, 2024
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131 changes: 83 additions & 48 deletions docs/tutorial.rst
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Expand Up @@ -27,21 +27,13 @@ explained later on.

.. image:: images/options_fig_wm.png

To showcase its functionalities we will load some example data using a dictionary, however Pyranges
includes a series of data loading options like gff, gtf, bam... (take a look at `Pyranges documentation <https://pyranges1.readthedocs.io/en/latest/>`_
to know more!).
To showcase its functionalities we will load some example data included in the Pyranges Plot package,
however Pyranges provides a series of data loading options like gff, gtf, bam... (take a look
at `Pyranges documentation <https://pyranges1.readthedocs.io/en/latest/>`_ to know more!).

.. code-block::
import pyranges as pr
p = pr.PyRanges({"Chromosome": [1, 1, 2, 2, 2, 2, 2, 3],
"Strand": ["+", "+", "-", "-", "+", "+", "+", "+"],
"Start": [1, 40, 10, 70, 85, 110, 150, 140],
"End": [11, 60, 25, 80, 100, 115, 180, 152],
"transcript_id":["t1", "t1", "t2", "t2", "t3", "t3", "t3", "t4"],
"feature1": ["a", "a", "b", "b", "c", "c", "c", "d"],
"feature2": ["A", "A", "B", "B", "C", "C", "C", "D"]})
p = prp.example_data.p1
print(p)
.. code-block::
Expand Down Expand Up @@ -207,25 +199,11 @@ values are accepted.
.. code-block::
# Store data
p_ala = pr.PyRanges({
"Start": [10, 50, 90] + [13, 60, 72, 120],
"End": [20, 75, 130] + [16, 63, 75, 123],
"Chromosome": [1]*7,
"id": ["gene1"]*7,
"trait1": ["exon"]*3 + ["aa"]*4 ,
"trait2": ["gene_1"]*3 + ["Ala"]*4,
"depth": [0]*3 + [1]*4,
})
p_cys = pr.PyRanges({
"Start": [10, 50, 90] + [15, 55, 62, 100, 110],
"End": [20, 75, 130] + [18, 58, 65, 103, 113],
"Chromosome": [1]*8,
"id": ["gene1"]*8,
"trait1": ["exon"]*3 + ["aa"]*5 ,
"trait2": ["gene_1"]*3 + ["Cys"]*5,
"depth": [0]*3 + [1]*5,
})
p_ala = prp.example_data.p_ala
p_cys = prp.example_data.p_cys
print(p_ala)
print(p_cys)
# Plot both PyRanges using depth to differentiate
prp.plot(
Expand All @@ -235,6 +213,38 @@ values are accepted.
thickness_col="trait1",
)
.. code-block::
index | Start End Chromosome id trait1 trait2 depth
int64 | int64 int64 int64 object object object int64
------- --- ------- ------- ------------ -------- -------- -------- -------
0 | 10 20 1 gene1 exon gene_1 0
1 | 50 75 1 gene1 exon gene_1 0
2 | 90 130 1 gene1 exon gene_1 0
3 | 13 16 1 gene1 aa Ala 1
4 | 60 63 1 gene1 aa Ala 1
5 | 72 75 1 gene1 aa Ala 1
6 | 120 123 1 gene1 aa Ala 1
PyRanges with 7 rows, 7 columns, and 1 index columns.
Contains 1 chromosomes.
index | Start End Chromosome id trait1 trait2 depth
int64 | int64 int64 int64 object object object int64
------- --- ------- ------- ------------ -------- -------- -------- -------
0 | 10 20 1 gene1 exon gene_1 0
1 | 50 75 1 gene1 exon gene_1 0
2 | 90 130 1 gene1 exon gene_1 0
3 | 15 18 1 gene1 aa Cys 1
4 | 55 58 1 gene1 aa Cys 1
5 | 62 65 1 gene1 aa Cys 1
6 | 100 103 1 gene1 aa Cys 1
7 | 110 113 1 gene1 aa Cys 1
PyRanges with 8 rows, 7 columns, and 1 index columns.
Contains 1 chromosomes.
.. image:: images/prp_rtd_11.png

Another way to highligh these overlapping regions playing with colors and depth.This time the
Expand Down Expand Up @@ -267,20 +277,31 @@ the "Feature" column of the data. A usage example is:

.. code-block::
pp = pr.PyRanges({
"Chromosome": [1, 1, 2, 2, 2, 2, 2, 3, 4, 4, 4, 4, 4, 4],
"Strand": ["+", "+", "-", "-", "+", "+", "+", "+", "-", "-", "-", "-", "+", "+"],
"Start": [1, 40, 10, 70, 85, 110, 150, 140, 30100, 30150, 30500, 30647, 29850, 29970],
"End": [11, 60, 25, 80, 100, 115, 180, 152, 30300, 30300, 30700, 30700, 29900, 30000],
"transcript_id": ["t1", "t1", "t2", "t2", "t3", "t3", "t3", "t4", "t5", "t5", "t5", "t5", "t6", "t6"],
"feature1": ["1", "1", "1", "1", "1", "2", "2", "2", "2", "2", "2", "2", "2", "2"],
"feature2": ["A", "A", "B", "B", "C", "C", "C", "D", "E", "E", "E", "E", "F", "F"],
"Feature": ["exon", "exon", "CDS", "CDS", "CDS", "CDS", "CDS", "exon", "exon", "CDS", "CDS", "exon", "CDS", "CDS"]
pp = prp.example_data.p2
})
print(pp)
prp.plot(pp, thick_cds=True)
.. code-block::
index | Chromosome Strand Start End transcript_id feature1 feature2 Feature
int64 | int64 object int64 int64 object object object object
------- --- ------------ -------- ------- ------- --------------- ---------- ---------- ---------
0 | 1 + 1 11 t1 1 A exon
1 | 1 + 40 60 t1 1 A exon
2 | 2 - 10 25 t2 1 B CDS
3 | 2 - 70 80 t2 1 B CDS
... | ... ... ... ... ... ... ... ...
10 | 4 - 30500 30700 t5 2 E CDS
11 | 4 - 30647 30700 t5 2 E exon
12 | 4 + 29850 29900 t6 2 F CDS
13 | 4 + 29970 30000 t6 2 F CDS
PyRanges with 14 rows, 8 columns, and 1 index columns.
Contains 4 chromosomes and 2 strands.
.. image:: images/prp_rtd_12.png


Expand All @@ -296,17 +317,31 @@ coordinate range, while when an int is given it will be interpreted as number of

.. code-block::
ppp = pr.PyRanges({'Chromosome': ['1'] * 10 + ['2'] * 10,
'Strand': ['+', '+', '+', '+', '-', '-', '-', '-', '+', '+'] + ["+", "+", "+", "+", "-", "-", "-", "-", "+", "+"],
'Start': [90, 61, 104, 228, 9, 142, 52, 149, 218, 151] + [5, 27, 37, 47, 1, 7, 42, 37, 60, 80],
'End': [92, 64, 113, 229, 12, 147, 57, 155, 224, 153] + [8, 32, 40, 50, 5, 10, 46, 40, 70, 90],
'transcript_id': ['t1', 't1', 't1', 't1', 't2', 't2', 't2', 't2', 't3', 't3'] + ["t4", "t4", "t4", "t4", "t5", "t5", "t5", "t5", "t6", "t6"],
'Feature': ["exon"] * 20
})
ppp = prp.example_data.p3
print(ppp)
prp.plot(ppp, shrink=True)
prp.plot(ppp, shrink=True, shrink_threshold=0.2)
.. code-block::
index | Chromosome Strand Start End transcript_id
int64 | object object int64 int64 object
------- --- ------------ -------- ------- ------- ---------------
0 | 1 + 90 92 t1
1 | 1 + 61 64 t1
2 | 1 + 104 113 t1
3 | 1 + 228 229 t1
... | ... ... ... ... ...
16 | 2 - 42 46 t5
17 | 2 - 37 40 t5
18 | 2 + 60 70 t6
19 | 2 + 80 90 t6
PyRanges with 20 rows, 5 columns, and 1 index columns.
Contains 2 chromosomes and 2 strands.
.. image:: images/prp_rtd_13.png
.. image:: images/prp_rtd_14.png

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1 change: 1 addition & 0 deletions src/pyranges_plot/__init__.py
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Expand Up @@ -13,3 +13,4 @@
)
from .plot_main import plot # noqa: F401
from .pr_register_plot import register_plot # noqa: F401
from .example_data import p1, p2, p3, p_ala, p_cys # noqa: F401

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