Intervene modules

Intervene provides three types of plots to visualize intersections of genomic regions and list sets. These are pairwise heatmap of N genomic region sets, classic Venn diagrams of genomic regions and list sets of up to 6-way and UpSet plots.

Venn diagram module

Once you have installed Intervene, you can type:

Usage:

intervene venn [options]

Note

Please scroll down to see a detailed summary of available options.

Help:

intervene venn --help

Example:

intervene venn -i path/to/BED/files/*.bed --type jaccard --htype tribar

This will save the results in the current working directory with a folder named Intervene_results. If you wish to save the results in a specific folder, you can type:

intervene venn -i path/to/BED/files/*.bed --type jaccard --htype tribar --output ~/results/path

Summary of options

Option	Description
-h, —help	To show the help message and exit
-i	Input genomic regions in (BED/GTF/GFF) format or lists of genes/SNPs IDs. For files in a directory use *.<extension>. e.g. *.bed
–type	{genomic,list}. Type of input data sets. Genomic regions or lists of genes/SNPs. Default is genomic
–names	Comma-separated list of names as labels for input files. Default is: –names=A,B,C,D,E,F
–filenames	Use file names as labels instead. Default is False
–colors	Comma-separated list of matplotlib-valid colors. E.g., –colors=r,b,k
-o, –output	Output folder path where results will be stored. Default is current working directory.
–figtype	{pdf,svg,ps,tiff,png} Figure type for the plot. e.g. –figtype svg. Default is pdf
–figsize	Figure size as width and height.e.g. –figsize 12 12.
–dpi	Dots-per-inch (DPI) for the output. Default is: 300
–fill	{number,percentage} Report number or percentage of overlaps (Only if –type=list). Default is number
–test	This will run the program on test data.

UpSet plot module

Once you have installed Intervene, you can type:

Usage:

intervene upset [options]

Note

Please scroll down to see a detailed summary of available options.

Help: You can also see list of options by typing this on the terminal.

intervene upset --help

Example:

intervene upset -i path/to/BED/files/*.bed --type jaccard --htype tribar

This will save the results in the current working directory with a folder named Intervene_results. If you wish to save the results in a specific folder, you can type:

intervene upset -i path/to/BED/files/*.bed --type jaccard --htype tribar --output ~/results/path

Summary of options

Option	Description
-h, –help	show this help message and exit
-i, –input	Input genomic regions in <BED/GTF/GFF/VCF> format or list files. For files in a directory use *.<ext>. e.g. *.bed
–type	Type of input sets. Genomic regions or lists of genes sets {genomic,list}. Default is genomic
–names	Comma-separated list of names for input files. Default is``–names=A,B,C,D,E,F``
–filenames	Use file names as labels instead. Default is False
-o, –output	Output folder path where plots will store. Default is current working directory.
–order	The order of intersections of sets {freq,degree}. e.g. –order degree. Default is freq
–ninter	Number of top intersections to plot. Default is 40
–showzero	Show empty overlap combinations. Default is False
–showsize	Show intersection sizes above bars. Default is False
–mbcolor	Color of the main bar plot. Default is gray23
–sbcolor	Color of set size bar plot. Default is #56B4E9
–mblabel	The y-axis label of the intersection size bars. Default is No of Intersections
–sxlabel	The x-axis label of the set size bars. Default is Set size
–figtype	Figure type for the plot. e.g. –figtype svg {pdf,svg,ps,tiff,png} Default is pdf
–figsize	Figure size for the output plot (width,height)
–dpi	Dots-per-inch (DPI) for the output. Default is 300
–run	Run Rscript if R and UpSetR package is installed. Default is True

Pairwise intersection module

Once you have installed Intervene, you can type:

Usage:

intervene pairwise [options]

Note

Please scroll down to see a detailed summary of available options.

Help:

intervene pairwise --help

Example:

intervene pairwise -i path/to/BED/files/*.bed --type jaccard --htype tribar

This will save the results in the current working directory with a folder named Intervene_results. If you wish to save the results in a specific folder, you can type:

intervene pairwise -i path/to/BED/files/*.bed --type jaccard --htype tribar --output ~/results/path

Summary of options

Option	Description
-h, –help	show this help message and exit
-i	Input genomic regions in (BED/GTF/GFF) format. For files in a directory use *.<extension>. e.g. *.bed
–type	Report count/fraction of overlaps or statistical relationships. {count frac jaccard fisher reldist}
	–type=count - calculates the number of overlaps.
	–type=frac - calculates the fraction of overlap.
	–type=jaccard - calculate the Jaccard statistic.
	–type=reldist - calculate the distribution of relative distances.
	–type=fisher - calculate Fisher`s statistic.
	Default is frac
–htype	{tribar,color,pie,circle,square,ellipse,number,shade}. Heatmap plot type. Default is pie.
–names	Comma-separated list of names for input files. Default is base name of input files.
–filenames	Use file names as labels instead. Default is False.
–sort	Set this only if your files are not sorted. Default is False.
–genome	Required argument if –type=fisher. Needs to be a string assembly name such as mm10 or hg38
-o, –output	Output folder path where results will be stored. Default is current working directory.
–barlabel	x-axis label of boxplot if –htype=tribar. Default is Set size
–barcolor	Boxplot color (hex vlaue or name, e.g. blue). Default is #53cfff.
–fontsize	Label font size. Default is 8.
–title	Heatmap main title. Default is Pairwise intersection
–space	White space between barplt and heatmap, if –htype=tribar. Default is 1.3.
–figtype	{pdf,svg,ps,tiff,png} Figure type for the plot. e.g. –figtype svg. Default is pdf
–figsize	Figure size for the output plot (width,height). e.g. –figsize 8 8
–dpi	Dots-per-inch (DPI) for the output. Default is: 300.
–test	This will run the program on test data.