plotLocReg

plotLocReg loads statistics generated by haplo_div to plot information of phased local region which calculates the local contacts ratio.

Usage

Usage:   perl HaploHiC.pl plotLocReg <[Options]>

Options:

  # plot phased local region information #

  # Inputs and Outputs #
   -dir     [s]  folder stores results of func 'haplo_div'. <required>
   -svg     [s]  svg figure output. <required>

  # Options #
   -max_lg  [s]  maximum size of local region. [2E7]
   -tmr_lg  [f]  ratio for unilateral trimming from largest local region size. [0.01]
   -tmr_pc  [f]  ratio for unilateral trimming from phased link counts. [0.01]
   -amt_fc  [s]  manually set the top of amount. [0]
   -rgb     [s]  rgb of heatmap color. ['255,0,0']

   -h|help       Display this help info.

Version:
   0.05 on 2019-04-08

Author:
   Wenlong Jia (wenlongkxm@gmail.com)

Inputs

plotLocReg gets the output folder path of haplo_div via option -dir, and automatically loads all merged statOfPhasedLocReg.gz.

In the header of merged statOfPhasedLocReg.gz, the unit of local region is declared.

Outputs

In the calculation of local contacts ratio, HaploHiC extends the local region with unit size till the phased contacts count reaches minimum. HaploHiC summaries how many Hi-C PE-reads with 'UK' end(s) are processed by certain phased contacts in local region with certain size, and plotLocReg plots this distribution. Here is one instance.