Merge pull request #15 from NelleV/doc

Better documentation.

CITATION

@@ -0,0 +1,12 @@
+To reference iced in publication, please cite the following:
+
+@Article{servant:hicpro,
+   Author="Servant, N.  and Varoquaux, N.  and Lajoie, B. R.  and Viara, E.
+   and Chen, C. J.  and Vert, J. P.  and Heard, E.  and Dekker, J.  and
+   Barillot, E. ",
+   Title="{{H}i{C}-{P}ro: an optimized and flexible pipeline for {H}i-{C} data processing}",
+   Journal="Genome Biol.",
+   Year="2015",
+   Volume="16",
+   Pages="259"
+  }

doc/index.rst

@@ -21,6 +21,22 @@ Contents:
    :maxdepth: 2
 
 
+References
+==========
+
+`HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
+<http://link.springer.com/article/10.1186/s13059-015-0831-x/fulltext.html>`_
+\*N. Servant, N. Varoquaux, B.R. Lajoie, E. Viara, C.J. Chen, J.-P. Vert, E.
+Heard, J. Dekker, E. Barillot, Genome Biology 2015 
+
+Contacts
+========
+
+If you have any questions or suggestions, please email nelle dot varoquaux at
+ensmp dot fr, or open a ticket on `Github
+<https://github.com/hiclib/pastis/issues>`_
+
+
 
 Indices and tables
 ==================

examples/utils/README.txt

@@ -0,0 +1,6 @@
+.. _utils_examples:
+
+Utils
+-------------
+
+Examples concerning the :mod:`iced.utils` module.

examples/utils/plot_extract_sample_map.py

@@ -20,7 +20,7 @@
 m = ax.matshow(sub_counts, cmap="Blues", norm=colors.SymLogNorm(1),
                origin="bottom",
                extent=(0, len(sub_counts), 0, len(sub_counts)))
-[ax.axhline(i, linewidth=1, color="#000000") for i in lengths.cumsum()]
-[ax.axvline(i, linewidth=1, color="#000000") for i in lengths.cumsum()]
+[ax.axhline(i, linewidth=1, color="#000000") for i in sub_lengths.cumsum()]
+[ax.axvline(i, linewidth=1, color="#000000") for i in sub_lengths.cumsum()]
 cb = fig.colorbar(m)
 ax.set_title("Chromosomes I, IV and V of yeast")

examples/utils/plot_intra_inter_contact_maps.py

@@ -0,0 +1,41 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib import colors
+
+from iced import datasets
+from iced.utils import get_intra_mask
+from iced.utils import get_inter_mask
+
+"""
+Extracting parts of a contact map.
+
+This examples shows how to use a mask to plot only the inter or the intra
+contact map.
+
+"""
+
+# Loading a sample dataset
+counts, lengths = datasets.load_sample_yeast()
+intra_mask = get_intra_mask(lengths)
+inter_mask = get_inter_mask(lengths)
+
+fig, axes = plt.subplots(ncols=2, figsize=(12, 6))
+inter_counts = counts.copy()
+inter_counts[intra_mask] = np.nan
+intra_counts = counts.copy()
+intra_counts[inter_mask] = np.nan
+
+m = axes[0].matshow(intra_counts, cmap="Blues", norm=colors.SymLogNorm(1),
+                    origin="bottom",
+                    extent=(0, len(counts), 0, len(counts)))
+m = axes[1].matshow(inter_counts, cmap="Blues", norm=colors.SymLogNorm(1),
+                    origin="bottom",
+                    extent=(0, len(counts), 0, len(counts)))
+
+axes[0].set_title("Intra-chromosomal maps")
+axes[1].set_title("Inter-chromosomal maps")
+
+[axes[0].axhline(i, linewidth=1, color="#000000") for i in lengths.cumsum()]
+[axes[0].axvline(i, linewidth=1, color="#000000") for i in lengths.cumsum()]
+[axes[1].axhline(i, linewidth=1, color="#000000") for i in lengths.cumsum()]
+[axes[1].axvline(i, linewidth=1, color="#000000") for i in lengths.cumsum()]