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.. _installation:
Installation
============
Requirements
------------
Loompy requires Python 3.6 or later. We recommend using `Anaconda Python <https://www.anaconda.com/download/>`_,
which can be installed in minutes, comes with all packages needed for scientific computing, and installs locally
in your home directory so you don't have to mess with your system's Python.
.. tip::
On Linux, many distributions already come with Python 3.6 or later. To find out which version you have,
and how to upgrade if necessary, please use `this guide <https://docs.python-guide.org/starting/install3/linux/>`_.
If you absolutely need to use an older Python, see below for how to install from source.
Easy installation
-----------------
Install the loompy package from PyPi with:
::
pip install -U loompy
.. tip::
The package is updated often (don't worry, the format is stable;
even in the rare occasion that you need to update your code, your old
loom files won't break). To ensure that you have the latest version, run
``pip install -U loompy`` again.
From source
-----------
Alternatively, you can install the latest version from source:
::
git clone https://github.com/linnarsson-lab/loompy.git
python setup.py install
If you just want to work with loom files within Python code, you should
be all set! We also made a web-app to make it easier to browse the data,
which you can install for local viewing, or set up for sharing loom
files from your own website. See the loom-viewer `repository <https://github.com/linnarsson-lab/loom-viewer/>`_ for more information.
If you need to use an older Python, `py-backwards <https://github.com/nvbn/py-backwards>`_ can be used
to backport loompy to at least Python 3.5. The following works, and creates a Python 3.5-compatible loompy:
.. code:: bash
cd ~/code/loompy # the loompy repository
git checkout 0f5c934679822c7babb020928516b9c7e01c3f7e # Checkout loompy that will work with 3.5
pip install py-backwards
cd ~/code # (the directory where loompy resides)
cp -R loompy loompy-3.5 # Make a copy of the repo
cd loompy-3.5/loompy
for f in *.py; do py-backwards -i $f -o $f -t 3.5; done # backport to Python 3.5
cd ..
py-backwards -i setup.py -o setup.py -t 3.5 # backport the setup script too
python setup.py install
.. warning::
Currently, a bug in py-backwards prevents the above from working properly for the
most recent versions of loompy. For that reason, the above script will check out an
older version that will convert to 3.5 without error. See https://github.com/nvbn/py-backwards/issues/48
.. _gettingstarted:
Getting Started
---------------
Go to http://loom.linnarssonlab.org and download one of the datasets. We will use ``cortex.loom`` below.
Run the following in a Jupyter notebook:
.. code:: python
>>> import loompy
>>> ds = loompy.connect("cortex.loom")
>>> ds
This shows the upper-left 10x10 corner of the matrix along with its
attributes:
.. raw:: html
<p>(18539, 1715)</p><table><tbody><tr><td> </td><td><strong>Cell_type</strong></td><td>eNb1</td><td>eNb1</td><td>eNb1</td><td>eNb1</td><td>eNb1</td><td>eNb1</td><td>eNb1</td><td>eNb1</td><td>eNb1</td><td>eNb1</td><td>...</td></tr><tr><td> </td><td><strong>Cell_ID</strong></td><td>1772122_301_C02</td><td>1772122_180_E05</td><td>1772122_300_H02</td><td>1772122_180_B09</td><td>1772122_180_G04</td><td>1772122_182_E09</td><td>1772122_302_C04</td><td>1772122_302_D11</td><td>1772122_180_C11</td><td>1772122_298_A07</td><td>...</td></tr><tr><td> </td><td><strong>Timepoint</strong></td><td>day_35</td><td>day_35</td><td>day_35</td><td>day_35</td><td>day_35</td><td>day_35</td><td>day_35</td><td>day_35</td><td>day_35</td><td>day_35</td><td>...</td></tr><tr><td><strong>Gene</strong></td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>...</td></tr><tr><td>DDX11L1</td><td> </td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>...</td></tr><tr><td>WASH7P_p1</td><td> </td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>...</td></tr><tr><td>LINC01002_loc4</td><td> </td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>...</td></tr><tr><td>LOC100133331_loc1</td><td> </td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>...</td></tr><tr><td>LOC100132287_loc2</td><td> </td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>...</td></tr><tr><td>LOC101928626</td><td> </td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>...</td></tr><tr><td>MIR6723</td><td> </td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>...</td></tr><tr><td>LOC100133331_loc2</td><td> </td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>...</td></tr><tr><td>LOC100288069_p1</td><td> </td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>...</td></tr><tr><td>FAM87B</td><td> </td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>0.0</td><td>...</td></tr><tr><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td></tr></tbody></table><br>
In this example, the total size of the dataset is 18539 rows (genes) by
1715 columns (cells). There are three column attributes (``Cell_type``,
``Cell_ID`` and ``Timepoint``) and one row attribute (``Gene``).
Next, try this:
.. code:: python
ds[ds.ra.Gene == "Actb", :]
This returns an array of the expression values for *Actb*. Note the use
of ``ds.ra.Gene == ...`` to pick out rows that match some
criterion, and the use of ds[..., ...] to select subsets of the data. In
this example, ``ds.ca.Gene == "Actb"`` is used as the row selector to pick
out the single row corresponding to *Actb*, and ``:`` is used to select
all columns. Hence, the expression returns the expression values for
*Actb* in every cell in the dataset.
Refer to the :ref:`API Walktrough <apiwalkthrough>` and the :ref:`API Documentation <fullapi>` to learn more about creating and
manipulating loom files.
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