================= 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:** .. code-block:: bash intervene venn [options] .. note:: Please scroll down to see a detailed summary of available **options**. **Help:** .. code-block:: bash intervene venn --help **Example:** .. code-block:: bash 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: .. code-block:: bash intervene venn -i path/to/BED/files/*.bed --type jaccard --htype tribar --output ~/results/path **Summary of options** .. csv-table:: :header: "Option", "Description" :widths: 10, 80 "-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 *.. 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:** .. code-block:: bash 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. .. code-block:: bash intervene upset --help **Example:** .. code-block:: bash 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: .. code-block:: bash intervene upset -i path/to/BED/files/*.bed --type jaccard --htype tribar --output ~/results/path **Summary of options** .. csv-table:: :header: "Option", "Description" :widths: 10,80 "-h, --help", "show this help message and exit" "-i, --input", "Input genomic regions in format or list files. For files in a directory use *.. 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:** .. code-block:: bash intervene pairwise [options] .. note:: Please scroll down to see a detailed summary of available **options**. **Help:** .. code-block:: bash intervene pairwise --help **Example:** .. code-block:: bash 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: .. code-block:: bash intervene pairwise -i path/to/BED/files/*.bed --type jaccard --htype tribar --output ~/results/path **Summary of options** .. csv-table:: :header: "Option", "Description" :widths: 10, 80 "-h, --help","show this help message and exit" "-i","Input genomic regions in (BED/GTF/GFF) format. For files in a directory use *.. 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."