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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).

intervene venn -i ~/ENCODE/data/H3K27ac.bed ~/ENCODE/data/H3Kme3.bed ~/ENCODE/data/H3K27me3.bed --filenames
3-way Venn diagram

By adding one more BED file to -i argument, Intervene will generate a 4-way Venn diagram of overlap of ChIP-seq peaks.

intervene venn -i ~/ENCODE/data/H3K27ac.bed ~/ENCODE/data/H3Kme3.bed ~/ENCODE/data/H3K27me3.bed  ~/ENCODE/data/H3Kme2.bed --filenames
4-way Venn diagram

Read more about the venn diagrams module here:

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).

intervene upset -i ~/ENCODE/data/H3K27ac.bed ~/ENCODE/data/H3Kme3.bed ~/ENCODE/data/H3K27me3.bed ~/ENCODE/data/H3Kme2.bed --filenames
UpSet plot

Read more about the upset module:

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.

intervene pairwise -i ~/dbSUPER/mm9/*.bed --filenames --compute frac --htype pie
Pairwise heatmap

By setting the --htype to color will produce this plot.

intervene pairwise -i ~/dbSUPER/mm9/*.bed --filenames --compute frac --htype color
Pairwise heatmap

By setting the --htype to tribar will produce a triangular heatmap and with a bar-plot of set sizes.

intervene pairwise -i ~/dbSUPER/mm9/*.bed --filenames --compute frac --htype tribar
Pairwise heatmap

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:

intervene pairwise --help