Synthetic Data

In [6]:

import sys
sys.path.append('../')

import sys sys.path.append('../')

In [7]:

from dlem.api import (jax_forward_generate, 
                        compute_contact_heatmap,
                        plot_map,
                        flip_diag_row)
from dlem.core import (normalize_expected_observed)
import jax 

from dlem.api import (jax_forward_generate, compute_contact_heatmap, plot_map, flip_diag_row) from dlem.core import (normalize_expected_observed) import jax

In [8]:

key = jax.random.PRNGKey(42)
n = 1000
resolution = 100
slowdown = .0025
rows = 200

key = jax.random.PRNGKey(42) n = 1000 resolution = 100 slowdown = .0025 rows = 200

In [9]:

p_left = jax.random.uniform(key, shape=(n,))
p_right = jax.random.uniform(key, shape=(n,))

p_left = jax.random.uniform(key, shape=(n,)) p_right = jax.random.uniform(key, shape=(n,))

In [10]:

out_data = jax_forward_generate(p_left, p_right, slowdown, rows)

out_data = jax_forward_generate(p_left, p_right, slowdown, rows)

In [11]:

out_data.shape

out_data.shape

Out[11]:

(200, 1000)

In [12]:

log = True
norm = normalize_expected_observed(out_data, log=log)

log = True norm = normalize_expected_observed(out_data, log=log)

In [13]:

import jax.numpy as jnp

padded_arr = jnp.pad(norm, 
                    pad_width=((0, n-rows)), 
                    mode='constant', 
                    constant_values=0)
prepared = flip_diag_row(padded_arr)

import jax.numpy as jnp padded_arr = jnp.pad(norm, pad_width=((0, n-rows)), mode='constant', constant_values=0) prepared = flip_diag_row(padded_arr)

In [14]:

chrom = "chr1"
start = 1
end = n*resolution
fig = plot_map(prepared, p_left, p_right, f'{chrom}:{start}-{end}', resolution)

chrom = "chr1" start = 1 end = n*resolution fig = plot_map(prepared, p_left, p_right, f'{chrom}:{start}-{end}', resolution)

In [15]:

plot_width = 700
fig.update_layout(
    width=plot_width,
    height=plot_width*1.61803,
)
file_path = f"synthetic_data_plotly.html"
fig.write_html(file_path)

plot_width = 700 fig.update_layout( width=plot_width, height=plot_width*1.61803, ) file_path = f"synthetic_data_plotly.html" fig.write_html(file_path)

In [16]:

from IPython.display import HTML, display

display(HTML("<style>.container { width:100% !important; }</style>"))
display(HTML(filename='../docs/synthetic_data_plotly.html'))

from IPython.display import HTML, display display(HTML("")) display(HTML(filename='../docs/synthetic_data_plotly.html'))