Example gallery¶
Here we listed some examples to demonstrate how Intervene can be used to generated 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
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
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
Read more about the upset
module:
In this example ...
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 upset -i ~/dbSUPER/mm9/*.bed --filenames --type frac --htype pie
By setting the --htype
to color
will produce this plot.
intervene upset -i ~/dbSUPER/mm9/*.bed --filenames --type frac --htype color
Read more about the pairwise
module here:
intervene pairwise --help