LoopWidth

Python package that produces piecharts and violin plots for visualizing chromatin loop widths from any file in paired bed format.

LoopWidth_piechart

Creates a piechart showing loop width distribution in any matplotlib-accepted format.

Requirements

• python >= 3.7
• pandas
• matplotlib

Usage

python LoopWidth_piechart.py  --loop <bedpe file> --bins <user-defined bin widths>  --res <bedpe resolution> --output <path to output piechart>

Parameters

• --loop: REQUIRED loop file in bedpe format (see bedtools documentation for more information), with a header row.
• --bins: OPTIONAL string of comma-separated user-defined resolution bins for loop widths to be binned into. Will also be used as the labels for the piechart. The ranges must start with one coordinate (ex. 1Mb) followed by a range (ex. 1Mb-4Mb), ending with one coordinate (4Mb+) with a '+' symbol at the end of the last coordinate. The coordinates may be in basepair format or Kb/Mb format (i.e 10000 or 10Kb). The first coordinate will be interpreted as "less than or equal to", and the last coordinate will be interpreted as "greater than". See example below for more information regarding the accepted format.
• --res: OPTIONAL integer input of loop file resolution. Must be 10000, 25000, 50000, or 100000. Pre-defined bins according to the resolution will be used, if different bins are preferred use the --bins argument.
• --output: REQUIRED file path to outputted piechart in any matplotlib accepted format (see matplotlib picture formats for more information)

NOTE: Either --bins or --res argument MUST be supplied, if both are supplied then the res argument will take precedence, as the allowed values for --res have predefined default bin values. The --bins argument should be used if the default bins for the resolution are not suitable to the data, or the data is in a different resolution.

Examples:

python LoopWidth_piechart.py  --loop Examples/test_loop_file.bedpe --bins 1Mb,1Mb-3Mb,3Mb-6Mb,6Mb+ --output Examples/piechart_bins_example.png

python LoopWidth_piechart.py  --loop Examples/test_loop_file.bedpe --res 100000 --output Examples/piechart_res_example.png

LoopWidth_violinplot

Creates a violin plot and outputs the log2(width) mean and median for bedpe file(s).

Requirements

• python >= 3.7
• pandas
• matplotlib
• seaborn
• statistics

Usage

python LoopWidth_violinplot.py --loop <bedpe file(s)> --labels <plot label(s)> --figWidth <figure width> --figHeight <figure height> --output <path to violinplot output>

Parameters

• --loop: REQUIRED loop file(s) in bedpe format (see bedtools documentation for more information), with a header row. If multiple loop files are to be plotted on the same plot, enter loop file paths separated by commas.
• --labels: REQUIRED labels for violin plot(s) corresponding to the order given in the loop parameter. If multiple, separate with commas.
• --output: REQUIRED file path to outputted violin plot in any matplotlib accepted format (see matplotlib picture formats for more info)
• --figWidth: OPTIONAL figure width in integer format. Default is 7.
• --figHeight: OPTIONAL figure height in integer format. Default is 7.

Examples:

python LoopWidth_violinplot.py --loop Examples/test_loop_file.bedpe,Examples/test_loop_file2.bedpe --labels test1,test2 --output Examples/violin_plot_multiple_files_example.png

Output:

Mean Log2(width) for Examples/test_loop_file.bedpe is: 21.782055367961732

Median Log2(width) for Examples/test_loop_file.bedpe is: 22.05248866110651

Mean Log2(width) for Examples/test_loop_file2.bedpe is: 22.51408577126218

Median Log2(width) for Examples/test_loop_file2.bedpe is: 22.620867729860066

python LoopWidth_violinplot.py --loop Examples/test_loop_file.bedpe --labels test1 --output Examples/violin_plot_one_file_example.png --figWidth 6 --figHeight 4

Output:

Mean Log2(width) for Examples/test_loop_file.bedpe is: 21.782055367961732

Median Log2(width) for Examples/test_loop_file.bedpe is: 22.05248866110651