=============== Example gallery =============== Here we provide some examples of how Intervene can be used to generate different types of set intersection plots. Venn module examples ==================== In this example, a 3-way Venn diagram of ChIP-seq peaks of histone modifications (H3K27ac, H3Kme3 and H3K27me3) in hESC from ENCODE data (Dunham et al., 2012). .. code-block:: bash intervene venn -i ~/ENCODE/data/H3K27ac.bed ~/ENCODE/data/H3Kme3.bed ~/ENCODE/data/H3K27me3.bed --filenames .. figure:: img/venn3way.png :height: 200px :alt: 3-way Venn diagram :align: center By adding one more BED file to ``-i`` argument, Intervene will generate a 4-way Venn diagram of overlap of ChIP-seq peaks. .. code-block:: bash intervene venn -i ~/ENCODE/data/H3K27ac.bed ~/ENCODE/data/H3Kme3.bed ~/ENCODE/data/H3K27me3.bed ~/ENCODE/data/H3Kme2.bed --filenames .. figure:: img/venn4way.png :height: 300px :alt: 4-way Venn diagram :align: center Read more about the ``venn`` diagrams module here: .. code-block:: bash intervene venn --help UpSet module examples ===================== In this example, a UpSet plot of ChIP-seq peaks of four histone modifications (H3K27ac, H3Kme3 H3Kme2, and H3K27me3) in hESC from ENCODE data (Dunham et al., 2012). .. code-block:: bash intervene upset -i ~/ENCODE/data/H3K27ac.bed ~/ENCODE/data/H3Kme3.bed ~/ENCODE/data/H3K27me3.bed ~/ENCODE/data/H3Kme2.bed --filenames .. figure:: img/upset4.png :height: 400px :alt: UpSet plot :align: center Read more about the ``upset`` module: .. code-block:: bash intervene upset --help Pairwise module examples ======================== In this example, we performed a pairwise intersections of super-enhancers in 24 mouse cell and tissue types from dbSUPER (Khan and Zhang, 2016) and showed the fraction of overlap in heatmap. .. code-block:: bash intervene pairwise -i ~/dbSUPER/mm9/*.bed --filenames --compute frac --htype pie .. figure:: img/pairwise_pie.png :height: 500px :alt: Pairwise heatmap :align: center By setting the ``--htype`` to ``color`` will produce this plot. .. code-block:: bash intervene pairwise -i ~/dbSUPER/mm9/*.bed --filenames --compute frac --htype color .. figure:: img/pairwise_color.png :height: 500px :alt: Pairwise heatmap :align: center By setting the ``--htype`` to ``tribar`` will produce a triangular heatmap and with a bar-plot of set sizes. .. code-block:: bash intervene pairwise -i ~/dbSUPER/mm9/*.bed --filenames --compute frac --htype tribar .. figure:: img/pairwise_tribar.png :height: 500px :alt: Pairwise heatmap :align: center .. note:: Please make sure that the ``tribar`` will only show lower triangle of the matrix as heatmap and diagoals are set to zero. It recommended to use this if ``--compute is set to ``jaccard``, ``fisher`` or ``reldist``. Read more about the ``pairwise`` module here: .. code-block:: bash intervene pairwise --help