# 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.
<img src="/img/fig0.svg">
### Installation (with Conda environment)
You can install `phic` in a clean environment as follows:
conda create -n phic python=3.12
conda activate phic
pip install phic
Without preparing a Python environment, PHi-C2 (=<2.0.13) rus on [Google Colab](https://bit.ly/3rlptGI).
### Requirements
- PHi-C2 is based on `python3`.
- Python packages `numpy`, `matplotlib`, `scipy`, `numba`, `click`, `pandas`, `hic-straw`, `cooler`, `h5py`.
To visualize the simulated polymer dynamics and conformations, [VMD](https://www.ks.uiuc.edu/Research/vmd/) is needed.
### Citation
If you use PHi-C2, please cite:
Soya Shinkai, Hiroya Itoga, Koji Kyoda, and Shuichi Onami. (2022).
**PHi-C2: interpreting Hi-C data as the dynamic 3D genome state.**
[_Bioinformatics_ **38**(21) 4984–4986](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac613/6695219).
<!--
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](https://doi.org/10.1093/nargab/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](https://doi.org/10.1016/j.bpj.2020.02.020). -->
### Quick Start
After the installation of `phic` and downloading of the directory [_demo_](/demo), move to the directory [_demo_](/demo):
demo/
run.sh
Then, execute the following script:
./run.sh
This process may take a few minutes.
The demo uses Hi-C data of mouse embryonic stem cells (chr8: 42,100–44,525 kb, 25-kb resolution, KR normalization) by [Bonev et al.](https://doi.org/10.1016/j.cell.2017.09.043).
* * *
### Usage
`phic` needs a subcommand on the command line interface:
phic SUBCOMMAND [OPTIONS]
Subcommands:
fetch-fileinfo
|
preprocessing
|
optimization
|--> plot-optimization
|--> dynamics
|--> sampling
|--> msd
| |--> plot-msd
|
|--> rheology
|--> plot-tangent
|--> plot-compliance
|--> plot-modulus
#### 0. fetch-fileinfo
phic fetch-fileinfo [OPTIONS]
Options:
--input TEXT Input Hi-C file (.hic or .mcool format) [required]
The `fetch-fileinfo` subcommand is used to inspect the basic metadata of a Hi-C data file.
As of version 2.1.1, `phic` supports both `.hic` and `.mcool` formats as input.
Use this command to check available chromosomes, resolution levels, and indexing details in the input file before proceeding with further analysis. This ensures that downstream subcommands reference the correct chromosome names and binning resolutions.
This is a recommended first step when working with new input files.
Example:
phic fetch-fileinfo --input FILENAME.hic
#### 1. preprocessing
phic preprocessing [OPTIONS]
Options:
--input TEXT Input Hi-C file (.hic or .mcool format) [required]
--res INTEGER Resolution of the bin size [required]
--plt-max-c FLOAT Maximum value of contact map [required]
--for-high-resolution INTEGER Normalization of contact map for high-resolution case (ex. 1-kb, 500-bp, 200-bp) [default=0]
--chr TEXT Target chromosome [required]
--grs INTEGER Start position of the target genomic region
--gre INTEGER End position of the target genomic region
--norm TEXT Type of normalization to apply
--tolerance FLOAT Threshold used to remove segments containing NaN values [required]
--help Show this message and exit.
In version 2.1.1 and later, the input data format has been changed to `.hic` or `.mcool`. Additionally, it is now possible to exclude rows and columns containing NaN values from the analysis by specifying their allowed proportion (ranging from 0 to 1) using the `tolerance` parameter.
When using the `preprocessing` subcommand, a directory will be automatically created based on the input Hi-C file name, chromosome number, genomic region of interest (optional), resolution, and normalization method. All subsequent analysis results will be stored in this directory. In the following explanations, we refer to this directory as _NAME_.
The outputs are as follows:
NAME/
C_normalized.svg
C_normalized.txt
P_normalized.svg
P_normalized.txt
_meta_data/
Example:
phic preprocessing --input FILENAME.hic --res 25000 --plt-max-c 0.1 --chr 8 --grs 42100000 --gre 44525000 --norm KR --tolerance 0.6
phic preprocessing --input FILENAME.hic --res 250000 --plt-max-c 0.1 --chr 8 --norm KR --tolerance 0.6
<img src="/img/fig1.svg" height="250">
#### 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]
--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 FLOAT Maximum and minimum values of optimized K map [required]
--help Show this message and exit.
The outputs are the followings:
NAME/data_optimization/
C.svg
C_optimized.txt
Correlation.png
Correlation_distance_corrected.png
Cost.svg
K.svg
P.svg
Example:
phic plot-optimization --name NAME --res 25000 --plt-max-c 0.1 --plt-max-k 0.1
<img src="/img/fig2.svg" height="500">
#### 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. msd
phic msd [OPTIONS]
Options:
--name TEXT Target directory name [required]
--upper INTEGER Upper value of the exponent of the normalized time [default=5]
--lower INTEGER Lower value of the exponent of the normalized time [default=-1]
--help Show this message and exit.
The outputs are the followings:
NAME/data_MSD/
n{BEAD-NUMBER}.txt
Example:
phic msd --name NAME
#### 3-4-2. plot-msd
phic plot-msd [OPTIONS]
Options:
--name TEXT Target directory name [required]
--upper INTEGER Upper value of the exponent of the normalized time [default=5]
--lower INTEGER Lower value of the exponent of the normalized time [default=-1]
--plt-upper INTEGER Upper value of the exponent of the normalized time in the spectrum [required]
--plt-lower INTEGER Lower value of the exponent of the normalized time in the spectrum [required]
--plt-max-log FLOAT Maximum value of log10 MSD [required]
--plt-min-log FLOAT Minimum value of log10 MSD [required]
--aspect FLOAT Aspect ratio of the spectrum [default=0.8]
--help Show this message and exit.
The output is the following:
NAME/data_MSD/
data_MSD_spectrum.txt
NAME/data_MSD/figs/
MSD_spectrum.svg
MSD_curves.png
Example:
phic plot-msd --name NAME --plt-upper 3 --plt-lower 0 --plt-max-log 2.0 --plt-min-log 0.5 --aspect 0.2
#### 3-5-1. 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/
data_normalized_omega1.txt
n{BEAD-NUMBER}.txt
Example:
phic rheology --name NAME
#### 3-5-2. 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
<img src="/img/fig5.svg" height="250">
#### 3-5-3. 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_storage_spectrum.txt
data_J_loss_spectrum.txt
data_J_abs_spectrum.txt
NAME/data_rheology/figs/
J_storage_spectrum.svg
J_loss_spectrum.svg
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
<img src="/img/fig3.svg" height="250">
#### 3-5-4. 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_storage_spectrum.txt
data_G_loss_spectrum.txt
data_G_abs_spectrum.txt
NAME/data_rheology/figs/
G_storage_spectrum.svg
G_loss_spectrum.svg
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
<img src="/img/fig4.svg" height="250">
Raw data
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"description": "# PHi-C2\nPHi-C2 allows for a physical interpretation of a Hi-C contact matrix.\nThe `phic` package includes a suite of command line tools.\n\n<img src=\"/img/fig0.svg\">\n\n### Installation (with Conda environment)\n\nYou can install `phic` in a clean environment as follows:\n\n conda create -n phic python=3.12\n conda activate phic\n pip install phic\n\n\n\n\n\nWithout preparing a Python environment, PHi-C2 (=<2.0.13) rus on [Google Colab](https://bit.ly/3rlptGI).\n\n### Requirements\n- PHi-C2 is based on `python3`.\n- Python packages `numpy`, `matplotlib`, `scipy`, `numba`, `click`, `pandas`, `hic-straw`, `cooler`, `h5py`.\n\nTo visualize the simulated polymer dynamics and conformations, [VMD](https://www.ks.uiuc.edu/Research/vmd/) is needed.\n\n\n### Citation\n\nIf you use PHi-C2, please cite:\n\nSoya Shinkai, Hiroya Itoga, Koji Kyoda, and Shuichi Onami. (2022).\n**PHi-C2: interpreting Hi-C data as the dynamic 3D genome state.**\n[_Bioinformatics_ **38**(21) 4984\u20134986](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac613/6695219).\n\n<!--\nWe will submit a manuscript on PHi-C2, in which we dramatically updated the algorithm of the optimization procedure.\nBut, the basic framework remains the same in the following papers:\n\n- 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](https://doi.org/10.1093/nargab/lqaa020).\n\n- 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\u20132228](https://doi.org/10.1016/j.bpj.2020.02.020). -->\n\n### Quick Start\n\nAfter the installation of `phic` and downloading of the directory [_demo_](/demo), move to the directory [_demo_](/demo):\n\n demo/\n run.sh\n\nThen, execute the following script:\n\n ./run.sh\n\nThis process may take a few minutes.\n\nThe demo uses Hi-C data of mouse embryonic stem cells (chr8: 42,100\u201344,525 kb, 25-kb resolution, KR normalization) by [Bonev et al.](https://doi.org/10.1016/j.cell.2017.09.043).\n\n* * *\n\n### Usage\n\n`phic` needs a subcommand on the command line interface:\n\n phic SUBCOMMAND [OPTIONS]\n\n Subcommands:\n fetch-fileinfo\n |\n preprocessing\n |\n optimization\n |--> plot-optimization\n |--> dynamics\n |--> sampling\n |--> msd\n | |--> plot-msd\n |\n |--> rheology\n |--> plot-tangent\n |--> plot-compliance\n |--> plot-modulus\n\n#### 0. fetch-fileinfo\n\n phic fetch-fileinfo [OPTIONS]\n\n Options:\n --input TEXT Input Hi-C file (.hic or .mcool format) [required]\n\nThe `fetch-fileinfo` subcommand is used to inspect the basic metadata of a Hi-C data file.\nAs of version 2.1.1, `phic` supports both `.hic` and `.mcool` formats as input.\n\nUse this command to check available chromosomes, resolution levels, and indexing details in the input file before proceeding with further analysis. This ensures that downstream subcommands reference the correct chromosome names and binning resolutions.\n\nThis is a recommended first step when working with new input files.\n\nExample:\n\n phic fetch-fileinfo --input FILENAME.hic\n\n#### 1. preprocessing\n\n phic preprocessing [OPTIONS]\n\n Options:\n --input TEXT Input Hi-C file (.hic or .mcool format) [required]\n --res INTEGER Resolution of the bin size [required]\n --plt-max-c FLOAT Maximum value of contact map [required]\n --for-high-resolution INTEGER Normalization of contact map for high-resolution case (ex. 1-kb, 500-bp, 200-bp) [default=0]\n --chr TEXT Target chromosome [required]\n --grs INTEGER Start position of the target genomic region\n --gre INTEGER End position of the target genomic region\n --norm TEXT Type of normalization to apply\n --tolerance FLOAT Threshold used to remove segments containing NaN values [required]\n --help Show this message and exit.\n\nIn version 2.1.1 and later, the input data format has been changed to `.hic` or `.mcool`. Additionally, it is now possible to exclude rows and columns containing NaN values from the analysis by specifying their allowed proportion (ranging from 0 to 1) using the `tolerance` parameter.\n\nWhen using the `preprocessing` subcommand, a directory will be automatically created based on the input Hi-C file name, chromosome number, genomic region of interest (optional), resolution, and normalization method. All subsequent analysis results will be stored in this directory. In the following explanations, we refer to this directory as _NAME_.\n\nThe outputs are as follows:\n\n NAME/\n C_normalized.svg\n C_normalized.txt\n P_normalized.svg\n P_normalized.txt\n _meta_data/\n\nExample:\n\n phic preprocessing --input FILENAME.hic --res 25000 --plt-max-c 0.1 --chr 8 --grs 42100000 --gre 44525000 --norm KR --tolerance 0.6\n phic preprocessing --input FILENAME.hic --res 250000 --plt-max-c 0.1 --chr 8 --norm KR --tolerance 0.6\n\n<img src=\"/img/fig1.svg\" height=\"250\">\n\n#### 2. optimization\n\n phic optimization [OPTIONS]\n\n Options:\n --name TEXT Target directory name [required]\n --init-k-backbone FLOAT Initial parameter of K_i,i+1 [default=0.5]\n --learning-rate FLOAT Learning rate [default=1e-4]\n --stop-condition-parameter FLOAT Parameter for the stop condition [default=1e-4]\n --help Show this message and exit.\n\n\nThe outputs are the followings:\n\n NAME/data_optimization/\n K_optimized.txt\n optimization.log\n\nExample:\n\n phic optimization --name NAME\n\n\n#### 3-1. plot-optimization\n\n phic plot-optimization [OPTIONS]\n\n Options:\n --name TEXT Target directory name [required]\n --res INTEGER Resolution of the bin size [required]\n --plt-max-c FLOAT Maximum value of contact map [required]\n --plt-max-k FLOAT Maximum and minimum values of optimized K map [required]\n --help Show this message and exit.\n\nThe outputs are the followings:\n\n NAME/data_optimization/\n C.svg\n C_optimized.txt\n Correlation.png\n Correlation_distance_corrected.png\n Cost.svg\n K.svg\n P.svg\n\nExample:\n\n phic plot-optimization --name NAME --res 25000 --plt-max-c 0.1 --plt-max-k 0.1\n\n<img src=\"/img/fig2.svg\" height=\"500\">\n\n\n#### 3-2. dynamics\n\n phic dynamics [OPTIONS]\n\n Options:\n --name TEXT Target directory name [required]\n --eps FLOAT Stepsize in the Langevin dynamics [default=1e-3]\n --interval INTEGER The number of steps between output frames [required]\n --frame INTEGER The number of output frames [required]\n --sample INTEGER The number of output dynamics [default=1]\n --seed INTEGER Seed of the random numbers [default=12345678]\n --help Show this message and exit.\n\nThe outputs are the followings:\n\n NAME/data_dynamics/\n polymer_N{NUMBER-OF-BEADS}.psf\n sample{SAMPLE-NUMBER}.xyz\n\nExample:\n\n phic dynamics --name NAME --interval 100 --frame 1000\n\n#### 3-3. sampling\n\n phic sampling [OPTIONS]\n\n Options:\n --name TEXT Target directory name [required]\n --sample INTEGER The number of output conformations [required]\n --seed INTEGER Seed of the random numbers [default=12345678]\n --help Show this message and exit.\n\nThe outputs are the followings:\n\n NAME/data_sampling/\n polymer_N{NUMBER-OF-BEADS}.psf\n conformations.xyz\n\nExample:\n\n phic sampling --name NAME --sample 1000\n\n#### 3-4-1. msd\n\n phic msd [OPTIONS]\n\n Options:\n --name TEXT Target directory name [required]\n --upper INTEGER Upper value of the exponent of the normalized time [default=5]\n --lower INTEGER Lower value of the exponent of the normalized time [default=-1]\n --help Show this message and exit.\n\nThe outputs are the followings:\n\n NAME/data_MSD/\n n{BEAD-NUMBER}.txt\n\nExample:\n\n phic msd --name NAME\n\n#### 3-4-2. plot-msd\n\n phic plot-msd [OPTIONS]\n\n Options:\n --name TEXT Target directory name [required]\n --upper INTEGER Upper value of the exponent of the normalized time [default=5]\n --lower INTEGER Lower value of the exponent of the normalized time [default=-1]\n --plt-upper INTEGER Upper value of the exponent of the normalized time in the spectrum [required]\n --plt-lower INTEGER Lower value of the exponent of the normalized time in the spectrum [required]\n --plt-max-log FLOAT Maximum value of log10 MSD [required]\n --plt-min-log FLOAT Minimum value of log10 MSD [required]\n --aspect FLOAT Aspect ratio of the spectrum [default=0.8]\n --help Show this message and exit.\n \nThe output is the following:\n\n NAME/data_MSD/\n data_MSD_spectrum.txt\n NAME/data_MSD/figs/\n MSD_spectrum.svg\n MSD_curves.png\n\nExample:\n\n phic plot-msd --name NAME --plt-upper 3 --plt-lower 0 --plt-max-log 2.0 --plt-min-log 0.5 --aspect 0.2\n\n#### 3-5-1. rheology\n\n phic rheology [OPTIONS]\n\n Options:\n --name TEXT Target directory name [required]\n --upper INTEGER Upper value of the exponent of the angular frequency [default=1]\n --lower INTEGER Lower value of the exponent of the angular frequency [default=-5]\n --help Show this message and exit.\n\nThe outputs are the followings:\n\n NAME/data_rheology/\n data_normalized_omega1.txt\n n{BEAD-NUMBER}.txt\n\nExample:\n\n phic rheology --name NAME\n\n#### 3-5-2. plot-tangent\n\n phic plot-tangent [OPTIONS]\n\n Options:\n --name TEXT Target directory name [required]\n --upper INTEGER Upper value of the exponent of the angular frequency [default=1]\n --lower INTEGER Lower value of the exponent of the angular frequency [default=-5]\n --plt-upper INTEGER Upper value of the exponent of the angular frequency in the spectrum [required]\n --plt-lower INTEGER Lower value of the exponent of the angular frequency in the spectrum [required]\n --plt-max-log FLOAT Maximum value of log10 tan\u03b4 [required]\n --aspect FLOAT Aspect ratio of the spectrum [default=0.8]\n --help Show this message and exit.\n\nThe output is the following:\n\n NAME/data_rheology/\n data_tan_spectrum.txt\n NAME/data_rheology/figs/\n tan_spectrum.svg\n\nExample:\n\n phic plot-tangent --name NAME --plt-upper 0 --plt-lower -3 --plt-max-log 0.2\n\n<img src=\"/img/fig5.svg\" height=\"250\">\n\n#### 3-5-3. plot-compliance\n\n phic plot-compliance [OPTIONS]\n\n Options:\n --name TEXT Target directory name [required]\n --upper INTEGER Upper value of the exponent of the angular frequency [default=1]\n --lower INTEGER Lower value of the exponent of the angular frequency [default=-5]\n --plt-upper INTEGER Upper value of the exponent of the angular frequency in the spectrum [required]\n --plt-lower INTEGER Lower value of the exponent of the angular frequency in the spectrum [required]\n --plt-max-log FLOAT Maximum value of log10 |J*| [required]\n --plt-min-log FLOAT Minimum value of log10 |J*| [required]\n --aspect FLOAT Aspect ratio of the spectrum [default=0.8]\n --help Show this message and exit.\n\nThe outputs are the followings:\n\n NAME/data_rheology/\n data_J_storage_spectrum.txt\n data_J_loss_spectrum.txt\n data_J_abs_spectrum.txt\n NAME/data_rheology/figs/\n J_storage_spectrum.svg\n J_loss_spectrum.svg\n J_abs_spectrum.svg\n J_curves.png\n\nExample:\n\n phic plot-compliance --name NAME --plt-upper 0 --plt-lower -3 --plt-max-log 1.3 --plt-min-log -0.3\n\n<img src=\"/img/fig3.svg\" height=\"250\">\n\n#### 3-5-4. plot-modulus\n\n phic plot-modulus [OPTIONS]\n\n Options:\n --name TEXT Target directory name [required]\n --upper INTEGER Upper value of the exponent of the angular frequency [default=1]\n --lower INTEGER Lower value of the exponent of the angular frequency [default=-5]\n --plt-upper INTEGER Upper value of the exponent of the angular frequency in the spectrum [required]\n --plt-lower INTEGER Lower value of the exponent of the angular frequency in the spectrum [required]\n --plt-max-log FLOAT Maximum value of log10 |G*| [required]\n --plt-min-log FLOAT Minimum value of log10 |G*| [required]\n --aspect FLOAT Aspect ratio of the spectrum [default=0.8]\n --help Show this message and exit.\n\nThe outputs are the followings:\n\n NAME/data_rheology/\n data_G_storage_spectrum.txt\n data_G_loss_spectrum.txt\n data_G_abs_spectrum.txt\n NAME/data_rheology/figs/\n G_storage_spectrum.svg\n G_loss_spectrum.svg\n G_abs_spectrum.svg\n G_curves.png\n\nExample:\n\n phic plot-modulus --name NAME --plt-upper 0 --plt-lower -3 --plt-max-log 0.4 --plt-min-log -1.2\n\n<img src=\"/img/fig4.svg\" height=\"250\">\n\n",
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