jloh plot

Description

Plot LOH propensity over all or specific chromosomes from multiple JLOH extract TSV output files.

Usage

jloh plot [--one-ref | --two-ref] --loh <TSV_1> ... <TSV_n> [options]

Parameters

Modes

--one-ref <BOOL>: Plot block propensity towards LOH or heterozygosity. Must be used in combination with --het parameter. This mode compares the regions with candidate LOH blocks with the regions with heterozygous blocks.

--two-ref <BOOL>: Plot LOH propensity towards genome A or B, with results obtained from jloh extract ran in --assign-blocks mode. This mode compares the blocks assigned to “REF” with those assigned to “ALT”.

Input / Output

Input

Choose one of these three options:

--loh [<PATH_1> ... <PATH_n>]: *.LOH_blocks.tsv output files produced by jloh extract.

--loh-files <PATH>: File of file names (.fofn) containing paths to *.LOH_blocks.tsv files produced by jloh extract, one per line. This option is an alternative to --loh.

--names-file <PATH>: TAB-separated file containing paths to *.LOH_blocks.tsv files produced by jloh extract, and an associated sample name. This option is an alternative to --loh.

--het <PATH>: *.exp.het_blocks.tsv output file produced by jloh extract. This file contains annotated heterozygous blocks and is needed only in --one-ref mode.

Output

--output-dir <PATH>: Path to the output directory.

--prefix <STR>: Prefix to include in output files.

Plot construction options

--ref-name <STR>: Name to use when labelling the reference (REF) allele.

--alt-name <STR>: Name to use when labelling the alternative (ALT) allele.

--by-sample <BOOL>: Produce a plot for each sample instead of a plot for each chromosome.

--merge <BOOL>: The output plot will combine all chromosomes into one.

--clusters <PATH>: Pass the output file produced by jloh cluster to sort the samples in the output plot according to the cluster.

--threads <INT>: Number of parallel workers to use in the plot table construction.

--chr <STR>: Restrict the analysis to this specific chromosome.

--chr-file <PATH>: Restrict the analysis to these specific chromosomes (file with names, one per line).

--window-size <INT>: Size of the plotting chromosomal windows. Smaller windows are more precise but slower to build.

--contrast <STR>

Increase plot contrast for samples with low LOH rate. Choose one of:

off (default): leave plot contrast untouched.
low: set contrast to “low”. This scales the LOH propensity to the 0 - 0.25 range.
mid: set contrast to “mid”. This scales the LOH propensity to the 0 - 0.50 range.
high: set contrast to “high”. This scales the LOH propensity to the 0 - 0.75 range.
max: set contrast to “max”. This scales the LOH propensity to the 0 - 1.00 range.

At the moment, this function works only with the --one-ref mode.

R / ggplot2 options

More info on some of these options can be found in the tidyverse official ggplot2 theme() manual. Colors are represented in HEX notation, find yours here.

--r-exec <PATH>: Path to the Rscript executable.

--aspect-ratio <FLOAT>: y/x length ratio.

--width <INT>: Plot width (px).

--height <INT>: Plot height (px).

--res <INT>: Plot resolution.

--het-color <STR>: Color to use to represent heterozygous blocks (#... HEX code).

--ref-color <STR>: Color to use to represent reference LOH blocks (#... HEX code).

--alt-color <STR>: Color to use to represent alternative LOH blocks (#... HEX code).

--midpoint-color <STR>: Color to use to represent the midpoint between ALT and REF (#... HEX code).