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Zhuoqing Fang committed May 28, 2017
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13 changes: 7 additions & 6 deletions docs/_build/html/_sources/run.rst.txt
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Expand Up @@ -27,16 +27,16 @@ The ``replot`` module reproduce GSEA desktop version results. The only input for
The ``call`` module produce GSEAPY results.
The ``gsea`` module produce GSEAPY results.

The input requries a txt file( FPKM, Expected Counts, TPM, et.al), a cls file,
and gene_sets file in gmt format.


.. code:: bash
# an example to compute using gseapy call module
$ gseapy call -d gsea_data.txt -c test.cls -g gene_sets.gmt
# an example to compute using gseapy gsea module
$ gseapy gsea -d gsea_data.txt -c test.cls -g gene_sets.gmt
Expand Down Expand Up @@ -80,7 +80,7 @@ This will import the following:
* The :func:`call` function to computing es,nes,pval,fdr,and generate plots *de novo*.
* The :func:`gsea` function to computing es,nes,pval,fdr,and generate plots *de novo*.

.. code:: python
Expand Down Expand Up @@ -110,14 +110,15 @@ To See help information of GSEAPY
$ gseapy --help
usage: gseapy [-h] [--version] {call,prerank,replot,enrichr} ...
usage: gseapy [-h] [--version] {gsea,prerank,single,replot,enrichr} ...
gseapy -- Gene Set Enrichment Analysis in Python
positional arguments:
{call,replot}
call Main GSEAPY Function: run GSEAPY instead of GSEA.
prerank Using pre-ranked tool to run GSEAPY.
single Run Single Sample GSEA.
replot Reproduce GSEA desktop figures.
enrichr Peform GSEA using enrichr API.
optional arguments:
Expand All @@ -136,7 +137,7 @@ For command line options of each command, type: gseapy COMMAND -h
$ gseapy replot -h
# or
$ gseapy call -h
$ gseapy gsea -h
# or
$ gseapy prerank -h
# or
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13 changes: 7 additions & 6 deletions docs/_build/html/run.html
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Expand Up @@ -194,11 +194,11 @@ <h2>For command line usage:<a class="headerlink" href="#for-command-line-usage"
$ gseapy replot -i ./gsea -o gseapy_out
</pre></div>
</div>
<p>The <code class="docutils literal"><span class="pre">call</span></code> module produce GSEAPY results.</p>
<p>The <code class="docutils literal"><span class="pre">gsea</span></code> module produce GSEAPY results.</p>
<p>The input requries a txt file( FPKM, Expected Counts, TPM, et.al), a cls file,
and gene_sets file in gmt format.</p>
<div class="code bash highlight-default"><div class="highlight"><pre><span></span># an example to compute using gseapy call module
$ gseapy call -d gsea_data.txt -c test.cls -g gene_sets.gmt
<div class="code bash highlight-default"><div class="highlight"><pre><span></span># an example to compute using gseapy gsea module
$ gseapy gsea -d gsea_data.txt -c test.cls -g gene_sets.gmt
</pre></div>
</div>
<p>The <code class="docutils literal"><span class="pre">prerank</span></code> module input expects a pre-ranked gene list dataset with correlation values, which in .rnk format,
Expand Down Expand Up @@ -230,7 +230,7 @@ <h2>Run gseapy inside python:<a class="headerlink" href="#run-gseapy-inside-pyth
</pre></div>
</div>
<ul class="simple">
<li>The <a class="reference internal" href="#gseapy.call" title="gseapy.call"><code class="xref py py-func docutils literal"><span class="pre">call()</span></code></a> function to computing es,nes,pval,fdr,and generate plots <em>de novo</em>.</li>
<li>The <code class="xref py py-func docutils literal"><span class="pre">gsea()</span></code> function to computing es,nes,pval,fdr,and generate plots <em>de novo</em>.</li>
</ul>
<div class="code python highlight-default"><div class="highlight"><pre><span></span><span class="c1"># An example to calculate es, nes, pval,fdrs, and produce figures using gseapy.</span>
<span class="n">gseapy</span><span class="o">.</span><span class="n">call</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="s1">&#39;gsea_dat.txt&#39;</span><span class="p">,</span> <span class="n">gene_sets</span><span class="o">=</span><span class="s1">&#39;gene_sets.gmt&#39;</span><span class="p">,</span> <span class="bp">cls</span><span class="o">=</span><span class="s1">&#39;test.cls&#39;</span><span class="p">,</span> <span class="n">outdir</span><span class="o">=</span><span class="s1">&#39;gseapy_out&#39;</span><span class="p">,</span>
Expand All @@ -255,14 +255,15 @@ <h2>To See help information of GSEAPY<a class="headerlink" href="#to-see-help-in
<h3>1. gseapy subcommands<a class="headerlink" href="#gseapy-subcommands" title="Permalink to this headline"></a></h3>
<div class="code bash highlight-default"><div class="highlight"><pre><span></span>$ gseapy --help

usage: gseapy [-h] [--version] {call,prerank,replot,enrichr} ...
usage: gseapy [-h] [--version] {gsea,prerank,single,replot,enrichr} ...

gseapy -- Gene Set Enrichment Analysis in Python

positional arguments:
{call,replot}
call Main GSEAPY Function: run GSEAPY instead of GSEA.
prerank Using pre-ranked tool to run GSEAPY.
single Run Single Sample GSEA.
replot Reproduce GSEA desktop figures.
enrichr Peform GSEA using enrichr API.
optional arguments:
Expand All @@ -276,7 +277,7 @@ <h3>1. gseapy subcommands<a class="headerlink" href="#gseapy-subcommands" title=
<h3>2. The subcommands help<a class="headerlink" href="#the-subcommands-help" title="Permalink to this headline"></a></h3>
<div class="code bash highlight-default"><div class="highlight"><pre><span></span>$ gseapy replot -h
# or
$ gseapy call -h
$ gseapy gsea -h
# or
$ gseapy prerank -h
# or
Expand Down
13 changes: 7 additions & 6 deletions docs/run.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -27,16 +27,16 @@ The ``replot`` module reproduce GSEA desktop version results. The only input for
The ``call`` module produce GSEAPY results.
The ``gsea`` module produce GSEAPY results.

The input requries a txt file( FPKM, Expected Counts, TPM, et.al), a cls file,
and gene_sets file in gmt format.


.. code:: bash
# an example to compute using gseapy call module
$ gseapy call -d gsea_data.txt -c test.cls -g gene_sets.gmt
# an example to compute using gseapy gsea module
$ gseapy gsea -d gsea_data.txt -c test.cls -g gene_sets.gmt
Expand Down Expand Up @@ -80,7 +80,7 @@ This will import the following:
* The :func:`call` function to computing es,nes,pval,fdr,and generate plots *de novo*.
* The :func:`gsea` function to computing es,nes,pval,fdr,and generate plots *de novo*.

.. code:: python
Expand Down Expand Up @@ -110,14 +110,15 @@ To See help information of GSEAPY
$ gseapy --help
usage: gseapy [-h] [--version] {call,prerank,replot,enrichr} ...
usage: gseapy [-h] [--version] {gsea,prerank,single,replot,enrichr} ...
gseapy -- Gene Set Enrichment Analysis in Python
positional arguments:
{call,replot}
call Main GSEAPY Function: run GSEAPY instead of GSEA.
prerank Using pre-ranked tool to run GSEAPY.
single Run Single Sample GSEA.
replot Reproduce GSEA desktop figures.
enrichr Peform GSEA using enrichr API.
optional arguments:
Expand All @@ -136,7 +137,7 @@ For command line options of each command, type: gseapy COMMAND -h
$ gseapy replot -h
# or
$ gseapy call -h
$ gseapy gsea -h
# or
$ gseapy prerank -h
# or
Expand Down

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