phic 2.0.1

Polymer dynamics deciphered from Hi-C data

PHi-C2

PHi-C2 allows for a physical interpretation of a Hi-C contact matrix. The phic package includes a suite of command line tools.

Installation

Install phic from PyPI using pip:

pip install phic

Without preparing a Python environment, PHi-C2 rus on Google Colab.

Requirements

• PHi-C2 is based on python3.
• Python packages numpy, matplotlib, scipy, numba, click.

To visualize the simulated polymer dynamics and conformations, VMD is needed.

Citation

We will submit a manuscript on PHi-C2, in which we dramatically updated the algorithm of the optimization procedure. But, the basic framework remains the same in the following papers:

• Soya Shinkai, Masaki Nakagawa, Takeshi Sugawara, Yuichi Togashi, Hiroshi Ochiai, Ryuichiro Nakato, Yuichi Taniguchi, and Shuichi Onami. (2020). PHi-C: deciphering Hi-C data into polymer dynamics. NAR Genomics and Bioinformatics 2 (2) lqaa020.

• Soya Shinkai, Takeshi Sugawara, Hisashi Miura, Ichiro Hiratani, and Shuichi Onami. (2020). Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization. Biophysical Journal 118 2220–2228.

Quick Start

After the installation of phic and downloading of the directory demo, move to the directory demo:

demo/
  Bonev_ES_observed_KR_chr8_42100-44500kb_res25kb.txt
  run.sh

Then, run the following scripts:

./run.sh

It will take a few minutes.

Here, Bonev_ES_observed_KR_chr8_42100-44500kb_res25kb.txt is an input file dumped by Juicertools with KR normalization for Hi-C data of mouse embryo stem cells (chr8: 42,100-44,525 kb, 25-kb resolution) by Bonev et al..

---

Usage

phic needs a subcommand on the command line interface:

phic SUBCOMMAND [OPTIONS]

Subcommands:
preprocessing
  |
optimization
  |-->  plot-optimization
  |-->  dynamics
  |-->  sampling
  |-->  rheology
          |--> plot-compliance
          |--> plot-modulus
          |--> plot-tangent

Here, NAME.txt as an ipunt is in sparse matrix format produced from “dump” command of Juicebox:

42100000	42100000	12899.836
42100000	42125000	2076.9636
42125000	42125000	11072.94
42100000	42150000	1264.3281
.............................
.............................
44475000	44500000	3374.337
44500000	44500000	10828.436

All output files of phic will be stored in the newly made directory NAME.

1. preprocessing

phic preprocessing [OPTIONS]

Options:
  --input     TEXT      Input file dumped by Juicertools for a hic file  [required]
  --res       INTEGER   Resolution of the bin size  [required]
  --plt-max-c FLOAT     Maximum value of contact map  [required]
  --help                Show this message and exit.

The outputs are the followings:

NAME/
  C.txt
  C_normalized.svg
  C_normalized.txt
  P_normalized.svg
  P_normalized.txt

Example:

phic preprocessing --input NAME.txt --res 25000 --plt-max-c 0.1

2. optimization

phic optimization [OPTIONS]

Options:
  --name                      TEXT   Target directory name  [required]
  --init-k-backbone           FLOAT  Initial parameter of K_i,i+1  [default=0.5]
  --learning-rate             FLOAT  Learning rate  [default=1e-4]
  --stop-condition-parameter  FLOAT  Parameter for the stop condition  [default=1e-4]
  --threads                   TEXT   The number of threads  [default=1]
  --help                             Show this message and exit.

The outputs are the followings:

NAME/data_optimization/
  K_optimized.txt
  optimization.log

Example:

phic optimization --name NAME

3-1. plot-optimization

phic plot-optimization [OPTIONS]

Options:
  --name                TEXT      Target directory name  [required]
  --res                 INTEGER   Resolution of the bin size  [required]
  --plt-max-c           FLOAT     Maximum value of contact map  [required]
  --plt-max-k-backbone  FLOAT     Maximum value of K_i,i+1 profile  [required]
  --plt-max-k           FLOAT     Maximum and minimum values of optimized K map  [required]
  --plt-k-dis-bins      INTEGER   The number of bins of distribution of optimized K values  [required]
  --plt-max-k-dis       FLOAT     Maximum value of the K distributioin  [required]
  --help                          Show this message and exit.

The outputs are the followings:

NAME/data_optimization/
  C.svg
  Correlation.png
  Cost.svg
  K.svg
  K_backbone.svg
  K_backbone.txt
  K_distribution.svg
  P.svg

Example:

phic plot-optimization --name NAME --res 25000 --plt-max-c 0.1 --plt-max-k-backbone 1.0 --plt-max-k 0.1 --plt-k-dis-bins 200 --plt-max-k-dis 100

3-2. dynamics

phic dynamics [OPTIONS]

Options:
  --name      TEXT      Target directory name  [required]
  --eps       FLOAT     Stepsize in the Langevin dynamics  [default=1e-3]
  --interval  INTEGER   The number of steps between output frames  [required]
  --frame     INTEGER   The number of output frames  [required]
  --sample    INTEGER   The number of output dynamics  [default=1]
  --seed      INTEGER   Seed of the random numbers  [default=12345678]
  --help                Show this message and exit.

The outputs are the followings:

NAME/data_dynamics/
  polymer_N{NUMBER-OF-BEADS}.psf
  sample{SAMPLE-NUMBER}.xyz

Example:

phic dynamics --name NAME --interval 100 --frame 1000

3-3. sampling

phic sampling [OPTIONS]

Options:
  --name    TEXT      Target directory name  [required]
  --sample  INTEGER   The number of output conformations  [required]
  --seed    INTEGER   Seed of the random numbers  [default=12345678]
  --help              Show this message and exit.

The outputs are the followings:

NAME/data_sampling/
  polymer_N{NUMBER-OF-BEADS}.psf
  conformations.xyz

Example:

phic sampling --name NAME --sample 1000

3-4-1. rheology

phic rheology [OPTIONS]

Options:
  --name    TEXT      Target directory name  [required]
  --upper   INTEGER   Upper value of the exponent of the angular frequency  [default=1]
  --lower   INTEGER   Lower value of the exponent of the angular frequency  [default=-5]
  --help              Show this message and exit.

The outputs are the followings:

NAME/data_rheology/
  n{BEAD-NUMBER}.txt

Example:

phic rheology --name NAME

3-4-2. plot-compliance

phic plot-compliance [OPTIONS]

Options:
  --name          TEXT      Target directory name  [required]
  --upper         INTEGER   Upper value of the exponent of the angular frequency  [default=1]
  --lower         INTEGER   Lower value of the exponent of the angular frequency  [default=-5]
  --plt-upper     INTEGER   Upper value of the exponent of the angular frequency in the spectrum  [required]
  --plt-lower     INTEGER   Lower value of the exponent of the angular frequency in the spectrum  [required]
  --plt-max-log   FLOAT     Maximum value of log10 |J*|  [required]
  --plt-min-log   FLOAT     Minimum value of log10 |J*|  [required]
  --aspect        FLOAT     Aspect ratio of the spectrum  [default=0.8]
  --help                    Show this message and exit.

The outputs are the followings:

NAME/data_rheology/
  data_J_abs_spectrum.txt
NAME/data_rheology/figs/
  J_abs_spectrum.svg
  J_curves.png

Example:

phic plot-compliance --name NAME --plt-upper 0 --plt-lower -3 --plt-max-log 1.3 --plt-min-log -0.3

3-4-2. plot-modulus

phic plot-modulus [OPTIONS]

Options:
  --name          TEXT      Target directory name  [required]
  --upper         INTEGER   Upper value of the exponent of the angular frequency  [default=1]
  --lower         INTEGER   Lower value of the exponent of the angular frequency  [default=-5]
  --plt-upper     INTEGER   Upper value of the exponent of the angular frequency in the spectrum  [required]
  --plt-lower     INTEGER   Lower value of the exponent of the angular frequency in the spectrum  [required]
  --plt-max-log   FLOAT     Maximum value of log10 |G*|  [required]
  --plt-min-log   FLOAT     Minimum value of log10 |G*|  [required]
  --aspect        FLOAT     Aspect ratio of the spectrum  [default=0.8]
  --help                    Show this message and exit.

The outputs are the followings:

NAME/data_rheology/
  data_G_abs_spectrum.txt
NAME/data_rheology/figs/
  G_abs_spectrum.svg
  G_curves.png

Example:

phic plot-modulus --name NAME --plt-upper 0 --plt-lower -3 --plt-max-log 0.4 --plt-min-log -1.2

3-4-3. plot-tangent

phic plot-tangent [OPTIONS]

Options:
  --name          TEXT      Target directory name  [required]
  --upper         INTEGER   Upper value of the exponent of the angular frequency  [default=1]
  --lower         INTEGER   Lower value of the exponent of the angular frequency  [default=-5]
  --plt-upper     INTEGER   Upper value of the exponent of the angular frequency in the spectrum  [required]
  --plt-lower     INTEGER   Lower value of the exponent of the angular frequency in the spectrum  [required]
  --plt-max-log   FLOAT     Maximum value of log10 tanδ  [required]
  --aspect        FLOAT     Aspect ratio of the spectrum  [default=0.8]
  --help                    Show this message and exit.

The output is the following:

NAME/data_rheology/
  data_tan_spectrum.txt
NAME/data_rheology/figs/
  tan_spectrum.svg

Example:

phic plot-tangent --name NAME --plt-upper 0 --plt-lower -3 --plt-max-log 0.2