diff --git a/doc/index.rst b/doc/index.rst index 91b2ae6..fb907b9 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -21,6 +21,22 @@ Contents: :maxdepth: 2 +References +========== + +`HiC-Pro: an optimized and flexible pipeline for Hi-C data processing +`_ +\*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 +`_ + + Indices and tables ================== diff --git a/examples/utils/README.txt b/examples/utils/README.txt new file mode 100644 index 0000000..4c4e0a2 --- /dev/null +++ b/examples/utils/README.txt @@ -0,0 +1,6 @@ +.. _utils_examples: + +Utils +------------- + +Examples concerning the :mod:`iced.utils` module. diff --git a/examples/utils/plot_extract_sample_map.py b/examples/utils/plot_extract_sample_map.py index a0c9bcf..4a11cf0 100644 --- a/examples/utils/plot_extract_sample_map.py +++ b/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") diff --git a/examples/utils/plot_intra_inter_contact_maps.py b/examples/utils/plot_intra_inter_contact_maps.py new file mode 100644 index 0000000..1e67db3 --- /dev/null +++ b/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()]