scHiCluster

https://github.com/zhoujt1994/schicluster
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A comprehensive Python package for single-cell chromosome contact data analysis, including cell type...
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### example

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_modules/example.html

Source code for example

```python
import time
import numpy as np
from schicluster import *
from sklearn.cluster import KMeans, SpectralClustering
from sklearn.metrics.cluster import adjusted_rand_score as ARI

[docs]('../api/example/index.html#example.mm9dim')mm9dim = [197195432, 181748087, 159599783, 155630120, 152537259, 149517037, 152524553, 131738871, 124076172, 129993255,
          121843856, 121257530, 120284312, 125194864, 103494974, 98319150, 95272651, 90772031, 61342430]

[docs]('../api/example/index.html#example.hg19dim')hg19dim = [249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747,
```

--------------------------------

### Directory and chromosome size setup

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/hba/plot_example.html

Sets up input/output directories and loads chromosome sizes.

```python
indir = '/data/hba/domain_majortype/'
ddir = f'/home/jzhou_salk_edu/sky_workdir/hba/domain_majortype/diff/{group_name}/'
ldir = f'/home/jzhou_salk_edu/sky_workdir/hba/loop_majortype/diff/{group_name}/'
cdir = f'/home/jzhou_salk_edu/sky_workdir/hba/compartment_majortype/diff/{group_name}/'

chrom_size_path = '/home/jzhou_salk_edu/sky_workdir/hba/ref/hg38.main.chrom.sizes'
chrom_sizes = cooler.read_chromsizes(chrom_size_path, all_names=True)
chrom_sizes = chrom_sizes.iloc[:-3]
```

--------------------------------

### Command Examples

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/command_line/hicluster_merge_cool.md

An example of how to use the hicluster merge-cool command.

```bash
hicluster merge-cool \
--input_cool_tsv_file impute/100K/cell_table_2.tsv \
--output_cool dataset/merge-cool.100kb
```

--------------------------------

### Command Example

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/command_line/hicluster_cpg_ratio.md

Example of calculating CpG ratio at each Chrom100K (resolution 100000).

```bash
hicluster cpg-ratio \
--fasta_path /data/aging/ref/m3C/mm10_with_chrl.fa \
--hdf_output_path cpg_ratio_100k.hdf \
--chrom_size_path /data/aging/ref/m3C/mm10.main.nochrM.nochrY.chrom.sizes \
--resolution 100000
```

--------------------------------

### Example 1: Imputation at 100kb resolution

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/command_line/hicluster_prepare_impute.md

This example shows how to prepare for imputation at 100kb resolution.

```bash
hicluster prepare-impute \
    --cell_table contact_table_rmbkl.tsv \
    --batch_size 1536 \
    --pad 1 \
    --cpu_per_job 30 \
    --chr1 1 \
    --pos1 2 \
    --chr2 5 \
    --pos2 6 \
    --output_dir impute/100K/ \
    --chrom_size_path /data/aging/ref/m3C/mm10.main.nochrM.nochrY.chrom.sizes \
    --output_dist 500000000 \
    --window_size 500000000 \
    --step_size 500000000 \
    --resolution 100000 \

```

--------------------------------

### Example 3: Imputation at 10kb resolution

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/command_line/hicluster_prepare_impute.md

This example shows how to prepare for imputation at 10kb resolution.

```bash
hicluster prepare-impute \
    --cell_table contact_table_rmbkl.tsv \
    --batch_size 1536 \
    --pad 1 \
    --cpu_per_job 30 \
    --chr1 1 \
    --pos1 2 \
    --chr2 5 \
    --pos2 6 \
    --output_dir impute/100K/ \
    --chrom_size_path /data/aging/ref/m3C/mm10.main.nochrM.nochrY.chrom.sizes \
    --output_dist 5050000 \
    --window_size 30000000 \
    --step_size 10000000 \
    --resolution 10000 \

```

--------------------------------

### Install scHiCluster

Source: https://github.com/zhoujt1994/schicluster/blob/master/README.md

Instructions for creating a conda environment and installing scHiCluster from GitHub.

```bash
conda create -n schicluster python==3.6.8
conda activate schicluster
pip install git+https://github.com/zhoujt1994/scHiCluster.git
```

--------------------------------

### Example 2: Imputation at 25kb resolution

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/command_line/hicluster_prepare_impute.md

This example shows how to prepare for imputation at 25kb resolution.

```bash
hicluster prepare-impute \
    --cell_table contact_table_rmbkl.tsv \
    --batch_size 1536 \
    --pad 1 \
    --cpu_per_job 30 \
    --chr1 1 \
    --pos1 2 \
    --chr2 5 \
    --pos2 6 \
    --output_dir impute/100K/ \
    --chrom_size_path /data/aging/ref/m3C/mm10.main.nochrM.nochrY.chrom.sizes \
    --output_dist 5050000 \
    --window_size 500000000 \
    --step_size 500000000 \
    --resolution 25000 \

```

--------------------------------

### Command Example

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/command_line/hicluster_contact_distance.md

An example of how to run the hicluster contact-distance command with specific parameters.

```bash
hicluster contact-distance \
--contact_table contact_table_rmbkl.tsv \
--chrom_size_path /data/aging/ref/m3C/mm10.main.nochrM.nochrY.chrom.sizes \
--output_prefix contact_distance \
--resolution 10000 \
--chr1 1 \
--pos1 2 \
--chr2 5 \
--pos2 6 \
--cpu 20

```

--------------------------------

### Command Example

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/command_line/hicluster_domain.html

An example of how to run the hicluster domain command.

```bash
hicluster domain \
--cell_table_path impute/25K/cell_table.tsv \
--output_prefix dataset/domain \
--resolution 25000 \
--window_size 10 \
--cpu 4
```

--------------------------------

### impute_cell command line examples

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_modules/impute_cell.html

These are example commands for running the impute_cell script with different parameters.

```bash
# command time python /gale/ddn/snm3C/humanPFC/code/impute_cell.py --indir /gale/raidix/rdx-5/zhoujt/projects/methylHiC/PFC_batch_merged/smoothed_matrix/1cell/${res0}b_resolution/chr${c}/ --outdir /gale/ddn/snm3C/humanPFC/smoothed_matrix/${res0}b_resolution/chr${c}/ --cell ${sample} --chrom ${c} --res ${res} --chrom_file /gale/netapp/home/zhoujt/genome/hg19/hg19.autosomal.chrom.sizes --mode pad2_std1_rp0.5_sqrtvc
# command time python /gale/ddn/snm3C/humanPFC/code/impute_cell.py --indir /gale/ddn/snm3C/humanPFC/cell_matrix/${res0}b_resolution/chr${c}/ --outdir /gale/ddn/snm3C/humanPFC/smoothed_matrix/${res0}b_resolution/chr${c}/ --cell ${sample} --chrom ${c} --res ${res} --chrom_file /gale/netapp/home/zhoujt/genome/hg19/hg19.autosomal.chrom.sizes --pad 2 --output_dist 10050000 --window_size 40000000 --step_size 10000000 --mode pad2_std1_rp0.5_ws40
```

--------------------------------

### Command Example

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/command_line/hicluster_embedding.md

An example command to generate a chromosome-by-chromosome contact matrix.

```bash
hicluster embedding \
    --cell_table_path cell_table.tsv \
    --output_dir dataset/embedding \
    --dim 50 \
    --dist 1000000 \
    --resolution 100000 \
    --scale_factor 100000 \
    --norm_sig \
    --save_raw \
    --cpu 20 
```

--------------------------------

### Command Time Example 1

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_modules/loop_mergechr.html

Example command for processing with loop_mergechr.

```bash
# command time python /gale/ddn/snm3C/humanPFC/code/loop_mergechr.py --inprefix /gale/ddn/snm3C/humanPFC/smoothed_matrix/10kb_resolution/merged/L23_${mode}_dist_trim/L23_${mode}_dist_trim --outprefix /gale/ddn/snm3C/humanPFC/smoothed_matrix/10kb_resolution/merged/L23_${mode}_dist_trim/L23_${mode}_dist_trim --chrom_file /gale/netapp/home/zhoujt/genome/hg19/hg19.autosomal.chrom.sizes
```

--------------------------------

### Command Line Usage Examples

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_modules/generatematrix_cell.html

Examples of how to run the generatematrix_cell script with different parameters.

```bash
python /gale/ddn/snm3C/humanPFC/code/generatematrix_cell.py --infile /gale/netapp/seq4/illumina_runs/ENTEx/Pool_BX_BY/mapping/output/TrCo_A9HOW_Plate1-1-H22/hic/TrCo_A9HOW_Plate1-1-H22-A13.3C.sorted_contacts_old.txt --outdir /gale/ddn/snm3C/humanPFC/cell_matrix/test/10kb_resolution/ --chrom_file /gale/netapp/home/zhoujt/genome/hg19/hg19.autosomal.chrom.sizes --split_file /gale/netapp/home/zhoujt/genome/hg19/hg19.chrsplit.bed --res 10000 --cell TrCo_A9HOW_Plate1-1-H22-A13
```

```bash
python /gale/ddn/snm3C/humanPFC/code/generatematrix_cell.py --infile /gale/netapp/seq4/illumina_runs/ENTEx/Pool_BX_BY/mapping/output/TrCo_A9HOW_Plate1-1-H22/hic/TrCo_A9HOW_Plate1-1-H22-A13.3C.sorted_contacts_old.txt --outdir /gale/ddn/snm3C/humanPFC/cell_matrix/test/100kb_resolution/ --chrom_file /gale/netapp/home/zhoujt/genome/hg19/hg19.autosomal.chrom.sizes --res 100000 --cell TrCo_A9HOW_Plate1-1-H22-A13
```

--------------------------------

### hicluster domain command example

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/command_line/hicluster_domain.md

An example of how to use the hicluster domain command.

```bash
hicluster domain \
--cell_table_path impute/25K/cell_table.tsv \
--output_prefix dataset/domain \
--resolution 25000 \
--window_size 10 \
--cpu 4 
```

--------------------------------

### Command Time Example 2

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_modules/loop_mergechr.html

Example command for processing and splitting with loop_mergechr.

```bash
# command time python /gale/ddn/snm3C/humanPFC/code/loop_mergechr.py --inprefix /gale/ddn/snm3C/humanPFC/smoothed_matrix/10kb_resolution/merged/L23_${mode}_dist_trim/L23_${mode}_dist_trim --outprefix /gale/ddn/snm3C/humanPFC/smoothed_matrix/10kb_resolution/merged/L23_${mode}_dist_trim/L23_${mode}_dist_trim.split --chrom_file /gale/netapp/home/zhoujt/genome/hg19/hg19.autosomal.chrom.sizes --split_file /gale/netapp/home/zhoujt/genome/hg19/hg19.chrsplit.bed
```

--------------------------------

### Command line execution example

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_modules/comp_cpg_cell.html

Example command to run the comp_cpg_cell script with specified parameters.

```bash
command time python /gale/ddn/snm3C/humanPFC/code/comp_cpg_cell.py --indir /gale/raidix/rdx-5/zhoujt/projects/methylHiC/PFC_batch_merged/smoothed_matrix/1cell/${res0}b_resolution/ --outdir /gale/ddn/snm3C/humanPFC/smoothed_matrix/${res0}b_resolution/ --cell $(cat /gale/ddn/snm3C/humanPFC/smoothed_matrix/celllist_long.txt | head -${SGE_TASK_ID} | tail -1) --chrom ${c} --mode raw --cpg_file /gale/ddn/snm3C/humanPFC/smoothed_matrix/${res0}b_resolution/bins/hg19.${res0}bin.CpG.txt
```

--------------------------------

### Calculate loop resolution

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/jupyter_execute/hba/plot_example.ipynb

Calculates the start and end indices for contact maps at a specified resolution.

```python
## contact maps are plotted at loop resolution
## select region to plot in Q matrix

resl = 10000
loopl, loopr = (ll//resl), (rr//resl)
print(loopl, loopr)
```

--------------------------------

### Define Directory Paths

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/hba/plot_example.ipynb

Sets up input and output directory paths for data processing.

```python
indir = '/data/hba/domain_majortype/'
ddir = f'/home/jzhou_salk_edu/sky_workdir/hba/domain_majortype/diff/{group_name}/'
ldir = f'/home/jzhou_salk_edu/sky_workdir/hba/loop_majortype/diff/{group_name}/'
cdir = f'/home/jzhou_salk_edu/sky_workdir/hba/compartment_majortype/diff/{group_name}/'
```

--------------------------------

### Select differential compartments

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/hba/plot_example.ipynb

Selects differential compartments based on chromosome, start position, and statistical significance.

```python
resc = 100000
comp = pd.read_csv(f'{cdir}DifferentialResult/fdr_result/differential.intra_sample_combined.pcQnm.bedGraph', sep='	', header=0, index_col=None)
comp.index = comp['chr'] + '_' + (comp['start'] // resc).astype(str)
bincomp = comp[['chr', 'start', 'end', 'sample_maha', 'pval', 'padj']]
comp = comp[leg]
selc = (bincomp['chr']==chrom) & (bincomp['start']>=ll) & (bincomp['start']<rr) & (zscore(bincomp['sample_maha'])>norm.isf(0.025))
print(selc.sum())
```

--------------------------------

### Thebe Kernel Configuration

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/api/setup/index.html

Configuration options for launching a Thebe kernel, including repository, kernel name, and CodeMirror settings.

```json
{
  "requestKernel": true,
  "binderOptions": {
    "repo": "binder-examples/jupyter-stacks-datascience",
    "ref": "master",
  },
  "codeMirrorConfig": {
    "theme": "abcdef",
    "mode": "python"
  },
  "kernelOptions": {
    "name": "python3",
    "path": "./api/setup"
  },
  "predefinedOutput": true
}
```

--------------------------------

### Example 1: Running the imputation command

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/command_line/hicluster_prepare_impute.md

This command generates the imputation cool files at 100kb resolution.

```bash
bash /home/qzeng_salk_edu/project/aging/230711_m3C/impute/100K/snakemake_cmd.txt 

```

--------------------------------

### Data Loading and Preparation

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_modules/example.html

Loads and prepares network, label, and CpG data for analysis.

```python
ctlist = ['HeLa', 'HAP1', 'GM12878', 'K562']
network = [np.loadtxt('1mb_resolution/' + ct + '/sample_list.txt', dtype=np.str) for ct in ctlist]
label = np.array([ctlist[i] for i in range(len(ctlist)) for j in range(len(network[i]))]).astype('U8')
network = np.concatenate(network)
chrom = [str(i + 1) for i in range(22)] + ['X']
chromsize = {chrom[i]: hg19dim[i] for i in range(len(chrom))}
nc = 4
cg = np.loadtxt('hg19/bin/hg19.1mb.bin.CpG.txt', dtype=np.str, skiprows=1, usecols=(0, 9, 11, 12))
cgdata = cg[:, 1:].astype(float)
cgdata = cgdata[:, 2] / (cgdata[:, 1] - cgdata[:, 0])
cgdata[np.isnan(cgdata)] = 0.0
chrcg = {c: cgdata[cg[:, 0] == 'chr' + c] for c in chrom}
```

--------------------------------

### Select differential boundaries

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/hba/plot_example.ipynb

Selects differential boundaries based on chromosome, start position, and various filtering criteria.

```python
binall = pd.read_hdf(f'{ddir}MajorType_boundary_stats.hdf', key='data')
selb = (binall['chrom']==chrom) & (binall['start']>=ll) & (binall['start']<rr) & binall['bklfilter'] & binall['chi2filter'] & binall['ins_lm'] & (binall['probdiff']>0.05) & binall['diff_sc']
print(selb.sum())
```

--------------------------------

### Determine genomic region for a gene

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/hba/plot_example.ipynb

Determines the genomic start and end coordinates for a given gene based on specified slopes.

```python
gtmp = 'LAMP5'
lslop, rslop = 1000000, 2000000

chrom = genemeta.loc[gtmp, 0]
if genemeta.loc[gtmp, 5]=='+':
    tss = genemeta.loc[gtmp, 1]
    tes = genemeta.loc[gtmp, 2]
else:
    tss = genemeta.loc[gtmp, 2]
    tes = genemeta.loc[gtmp, 1]

ll, rr = (tss - lslop), (tss + rslop)
print(chrom, ll, rr, genemeta.loc[gtmp, 5])
```

--------------------------------

### Figure and Axes Setup with Differential Plots

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/hba/plot_example.ipynb

This code sets up the figure and axes for plotting various genomic features, including Chi-Square, differential feature positions, boundary probabilities, and insulation scores.

```python
fig, axes = plt.subplots(len(leg)*2+1, 1, figsize=(10, np.sum([1] + np.tile([3.5,1],len(leg)).tolist())/2), 
                         gridspec_kw={'height_ratios':[1] + np.tile([3.5,1],len(leg)).tolist()}, dpi=300, sharex='all')

tmpl = loopall.loc[sell, [1,4]].values // resl - loopl
tmpd = binall.loc[selb, 'start'] // resl - loopl
tmpc = bincomp.loc[selc, 'start'] // resl - loopl

ax = axes[0]
sel = (binall['chrom']==chrom) & (binall['start']>=ll) & (binall['start']<rr)
xpos = (binall.loc[sel, 'start'] // resl - loopl) * np.sqrt(2)
ax.plot(xpos, binall.loc[sel, 'chi2_sc'].values, 
        c='C0', alpha=0.7)

ax.set_title('Chi-Square', fontsize=10)
ax.set_xlim([0, (loopr-loopl-1)*np.sqrt(2)])

for i in range(len(leg)):
    ax = axes[i*2+1]
    ax.set_title(legname[i], fontsize=10)
    ax.spines['right'].set_visible(False)
    ax.spines['top'].set_visible(False)
    ax.spines['bottom'].set_visible(False)
    ax.spines['left'].set_visible(False)
    img = ax.imshow(dstall[i], cmap='afmhot_r', vmin=0, vmax=0.012)
    h = len(dstall[i])
    ax.set_ylim([0.5*h, 0.4*h])
    ax.set_xlim([0, h])
    ax.set_yticks([])
    ax.set_yticklabels([])
    ax.scatter((tmpl[:, 0]+tmpl[:, 1])/np.sqrt(2), 0.5*h-(tmpl[:, 1]-tmpl[:, 0])/np.sqrt(2), 
           alpha=0.1, s=10, marker='D', edgecolors='c', color='none')

    ax = axes[i*2+2]
    ax.plot(xpos, bound_prob_ct.loc[leg[i], sel].values, c='C0', alpha=0.7)
    ax.scatter(tmpd * np.sqrt(2), np.zeros(len(tmpd))+0.05, color='r', s=4)
    ax.set_ylim([0, 0.3])
    ax2 = ax.twinx()
    ax2.plot(xpos, ins.loc[leg[i], sel].values, c='C1', alpha=0.7)
    ax2.set_ylim([0.05, 0.4])
    
ax.set_xlim([0, (loopr-loopl-1)*np.sqrt(2)])
ax.set_xticks(np.sqrt(2)*np.array(np.arange(0, loopr-loopl+1, 100).tolist() + [tss//resl-loopl, tes//resl-loopl]))
ax.set_xticklabels([])
ax.set_xticklabels([f'{(xx+loopl)/100}M' for xx in np.arange(0, loopr-loopl+1, 100)]+['TSS','TES'])

```

--------------------------------

### Pseudobulk Matrix Generation Setup

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/Tan2021/prepare.html

This code initializes parameters for pseudobulk matrix generation, defines chunk size, and reads a Snakefile template. It then iterates through cell groups, creating directories and preparing cell tables for each chunk, either as a single chunk or divided based on chunk_size.

```python
params = {
    'resolution': 25000,
    'chrom_size_path': '"/data/ref/mm10/genome/mm10.main20.chrom.sizes"',
}

chunk_size = 200
res = 25000
total_chunk_dirs = []
group_chunks = {}

with open(f'{PACKAGE_DIR}/cool/Snakefile_chunk_template') as tmp:
    GENERATE_MATRIX_CHUNK_TEMPLATE = tmp.read()

for group, group_df in cell_table.groupby('cluster'):
    group_chunks[group] = []
    if group_df.shape[0] <= chunk_size:
        this_dir = f'{outdir}{group}_chunk0/'
        params['cell_table_path'] = f'"{this_dir}cell_table.csv"'
        prepare_dir(this_dir, group_df, GENERATE_MATRIX_CHUNK_TEMPLATE, params)
        total_chunk_dirs.append(this_dir)
        group_chunks[group].append(this_dir)
    else:
        group_df['chunk'] = [i // chunk_size for i in range(group_df.shape[0])]
        for chunk, chunk_df in group_df.groupby('chunk'):
            this_dir = f'{outdir}{group}_chunk{chunk}/'
            params['cell_table_path'] = f'"{this_dir}cell_table.csv"'
            prepare_dir(this_dir, chunk_df, GENERATE_MATRIX_CHUNK_TEMPLATE, params)
            total_chunk_dirs.append(this_dir)
            group_chunks[group].append(this_dir)
            

with open(f'{outdir}snakemake_cmd_step1.txt', 'w') as f:
```

--------------------------------

### Define Input and Output Directories and Resolution

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/hba/domain_majortype/01.call.ipynb

Sets the input and output directory paths and the resolution for analysis.

```python
indir = '/data/hba/domain_majortype/'
outdir = '/home/jzhou_salk_edu/sky_workdir/hba/domain_majortype/'
res = 25000
```

--------------------------------

### install_r_package

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_modules/schicluster/domain/call_domain.html

Check if some R package is installed and install it if not.

```python
def install_r_package(name):
    if not isinstalled(name):
        utils = importr('utils')
        utils.chooseCRANmirror(ind=1)
        utils.install_packages(StrVector([name]))
```

--------------------------------

### Command line interface

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_modules/domain_insulation_cell.html

Example command to run the domain_insulation_cell script.

```bash
command time python /gale/ddn/snm3C/humanPFC/code/domain_insulation_cell.py --indir /gale/ddn/snm3C/humanPFC/smoothed_matrix/${res0}b_resolution/ --cell ${sample} --chrom ${c} --mode pad2_std1_rp0.5_sqrtvc --w 10
```

--------------------------------

### Argument parser setup

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_modules/domain_insulation_cell.html

This section shows how the command-line arguments are parsed.

```python
parser = argparse.ArgumentParser()
parser.add_argument('--indir', type=str, default=None, help='Directory of imputed matrices end with /')
parser.add_argument('--cell', type=str, default=None, help='Full path of a file containing a list of cell identifiers to be concatenate')
parser.add_argument('--chrom', type=str, default=None, help='Chromosome to impute')
parser.add_argument('--mode', type=str, default=None, help='Suffix of imputed matrix file names')
parser.add_argument('--w', type=int, default=10, help='Window size for insulation score')
opt = parser.parse_args()

domain_insulation_cell(opt.indir, opt.cell, opt.chrom, opt.mode, opt.w)
```

--------------------------------

### Command Examples

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_modules/loop_sumcell_chr.html

Examples of how to run the loop_sumcell_chr script with different parameters.

```bash
# mode=pad2_std1_rp0.5_sqrtvc
# command time python /gale/ddn/snm3C/humanPFC/code/loop_sumcell_chr.py --cell_list /gale/ddn/snm3C/humanPFC/smoothed_matrix/10kb_resolution/filelist/L23_covgroup${i}_${mode}_chr${c}_looplist.txt --outprefix /gale/ddn/snm3C/humanPFC/smoothed_matrix/10kb_resolution/merged/L23_covgroup${i}_${mode}_dist_trim/L23_covgroup${i}_${mode}_dist_trim_chr${c} --res 10000
# command time python /gale/ddn/snm3C/humanPFC/code/loop_sumcell_chr.py --cell_list /gale/ddn/snm3C/humanPFC/smoothed_matrix/10kb_resolution/filelist/L23_${mode}_chr${c}_looplist.txt --group_list /gale/ddn/snm3C/humanPFC/smoothed_matrix/10kb_resolution/filelist/L23_${mode}_chr${c}_grouplist.txt --outprefix /gale/ddn/snm3C/humanPFC/smoothed_matrix/10kb_resolution/merged/L23_${mode}_dist_trim/L23_${mode}_dist_trim_chr${c} --res 10000
```

--------------------------------

### Set input directory

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/jupyter_execute/hba/plot_example.ipynb

Sets the input directory path for loop data.

```python
indir = '/home/jzhou_salk_edu/sky_workdir/hba/loop_majortype/'
```

--------------------------------

### Example Usage

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/command_line/hicluster_filter_contact.html

An example of how to use the hicluster filter-contact command with various options.

```bash
--contact_table contact_table.tsv
--output_dir rmbkl
--blacklist_1d_path /data/aging/ref/m3C/mm10-blacklist.v2.bed.gz
--blacklist_2d_path /data/aging/ref/m3C/mm10_2d_blacklist.bed.gz
--chr1 1
--pos1 2
--chr2 5
--pos2 6
```

--------------------------------

### scHiCluster CPU

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_modules/example.html

Performs clustering using scHiCluster on CPU and evaluates with KMeans and SpectralClustering.

```python
start_time = time.time()
cluster, embedding = hicluster_cpu(network, chromsize, nc=nc, ncpus=5)
print(time.time() - start_time)
[ARI(label, KMeans(n_clusters=nc, n_init=200).fit(embedding[:, :ndim]).labels_) for ndim in [2, 5, 10, 20, 50]]
```

--------------------------------

### Kernel Configuration

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/api/example/index.html

Configuration for the Jupyter kernel, including request for kernel, binder options, CodeMirror configuration, and kernel options.

```json
{ requestKernel: true, binderOptions: { repo: "binder-examples/jupyter-stacks-datascience", ref: "master", }, codeMirrorConfig: { theme: "abcdef", mode: "python" }, kernelOptions: { name: "python3", path: "./api/example" }, predefinedOutput: true }
```

--------------------------------

### Directory and Chromosome Size Setup

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/hba/loop_majortype/01.diff.html

Sets input and output directories, resolution, and loads chromosome sizes and offsets for cooler objects.

```python
indir = '/home/jzhou_salk_edu/sky_workdir/hba/loop_majortype/'
outdir = '/home/jzhou_salk_edu/sky_workdir/hba/loop_majortype/'
res = 10000
group = group_name

chrom_size_path = f'{indir}hg38_with_chrl.main.chrom.sizes'
chrom_sizes = cooler.read_chromsizes(chrom_size_path, all_names=True)
bins_df = cooler.binnify(chrom_sizes, res)
chrom_offset = get_chrom_offsets(bins_df)
```

--------------------------------

### Module Contents

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/api/example/index.html

This section lists the contents of the module, including variables and their initial values.

```python
mm9dim _= [197195432, 181748087, 159599783, 155630120, 152537259, 149517037, 152524553, 131738871,...
```

```python
hg19dim _= [249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022,...
```

```python
ctlist _= ['HeLa', 'HAP1', 'GM12878', 'K562']
```

```python
network
```

```python
label
```

```python
network
```

```python
chrom
```

```python
chromsize
```

```python
nc _= 4
```

```python
cg
```

```python
cgdata
```

```python
cgdata
```

```python
chrcg
```

```python
start_time
```

```python
start_time
```

```python
start_time
```

```python
start_time
```

```python
start_time
```

```python
start_time
```

```python
start_time
```

```python
start_time
```

```python
start_time
```

```python
start_time
```

```python
start_time
```

--------------------------------

### Directory and Chromosome Size Setup

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/hba/loop_majortype/04.corr.html

Sets up input and output directories, resolution, and reads chromosome sizes for cooler.

```python
res = 10000

indir = '/home/jzhou_salk_edu/sky_workdir/hba/loop_majortype/'
outdir = f'/home/jzhou_salk_edu/sky_workdir/hba/loop_majortype/diff/{group_name}/'

chrom_size_path = f'{indir}hg38_with_chrl.main.chrom.sizes'
chrom_sizes = cooler.read_chromsizes(chrom_size_path, all_names=True)
```

--------------------------------

### Example 3: Imputation at 10kb resolution

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/command_line/hicluster_prepare_impute.html

This example demonstrates imputation at a 10kb resolution.

```bash
hicluster prepare-impute \
    --cell_table contact_table_rmbkl.tsv \
    --batch_size 1536 \
    --pad 1 \
    --cpu_per_job 30 \
    --chr1 1 \
    --pos1 2 \
    --chr2 5 \
    --pos2 6 \
    --output_dir impute/100K/ \
    --chrom_size_path /data/aging/ref/m3C/mm10.main.nochrM.nochrY.chrom.sizes \
    --output_dist 5050000 \
    --window_size 30000000 \
    --step_size 10000000 \
    --resolution 10000
```

--------------------------------

### Command Example

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/command_line/hicluster_filter_contact.md

An example of processing snm3C-seq data of mouse brain using the hicluster filter-contact command.

```bash
hicluster filter-contact \
    --output_dir rmbkl \
    --blacklist_1d_path /data/aging/ref/m3C/mm10-blacklist.v2.bed.gz \
    --blacklist_2d_path /data/aging/ref/m3C/mm10_2d_blacklist.bedpe.gz \
    --cpu 20 \
    --chr1 1 \
    --pos1 2 \
    --chr2 5 \
    --pos2 6 \
    --contact_table contact_table.tsv \
    --chrom_size_path /data/aging/ref/m3C/mm10.main.nochrM.nochrY.chrom.sizes
```

--------------------------------

### hicluster merge-cell-raw Example

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/command_line/hicluster_merge_cell_raw.md

This snippet provides an example of how to use the `hicluster merge-cell-raw` command with specific arguments.

```bash
hicluster merge-cell-raw \
--cell_table contact_table_rmbkl.tsv \
--chrom_size_path /data/aging/ref/m3C/mm10.main.nochrM.nochrY.chrom.sizes \
--output_file dataset/merge-cell-raw.5kb \
--resolution 5000 \
--chr1 1 \
--pos1 2 \
--chr2 5 \
--pos2 6 \
--min_pos_dist 2500
```

--------------------------------

### Load cell type Q matrices

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_sources/hba/plot_example.ipynb

Loads cell type Q matrices from cooler files and extracts a specific region.

```python
from scipy import ndimage as nd

dstall = []
for ct in leg:
    cool = cooler.Cooler(f'{indir}{ct}/{ct}/{ct}.Q.cool')
    Q = cool.matrix(balance=False, sparse=True).fetch(chrom).tocsr()
    tmp = Q[loopl:loopr, loopl:loopr].toarray()
    dstall.append(tmp)
    print(ct)
```

--------------------------------

### Data Processing Example

Source: https://github.com/zhoujt1994/schicluster/blob/master/doc/schicluster/_build/html/_modules/raw2mat.html

Example of reading CSV data, filtering, and processing columns.

```python
cell = sys.argv[3]

data = pd.read_csv(infile, sep='\t', header=None, index_col=None)
data = data[data[4]==data[5]]
data[4] = data[4].str.split('_', expand=True)[1]

data = data[data[4].isin(chromsize.keys())]

data[5] = data[4].map(size)
data[[0,1]] = data[[0,1]].values - data[5].values[:,None]
for c, tmp in data.groupby(by=4):
	tmp[[0,1,2]].astype(int).to_csv(f'{outdir}{c}/{cell}_{c}.txt', sep='\t', header=False, index=False)
```
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