metbit 7.3.4__py3-none-any.whl

metbit/STOCSY.py

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+# -*- coding: utf-8 -*-
+
+__auther__ ='aeiwz'
+author_email='theerayut_aeiw_123@hotmail.com'
+__copyright__="Copyright 2024, Theerayut"
+
+__license__ = "MIT"
+__maintainer__ = "aeiwz"
+__email__ = "theerayut_aeiw_123@hotmail.com"
+__status__ = "Develop"
+
+import numpy as np
+import pandas as pd
+import plotly.graph_objects as go
+from scipy.stats import pearsonr
+
+
+
+
+def STOCSY(spectra: pd.DataFrame, anchor_ppm_value, p_value_threshold=0.0001):
+
+    """
+    Performs a STOCSY (Statistic Total Correlation Spectroscopy) analysis on NMR spectra data.
+
+    This function calculates the Pearson correlation between a specified anchor signal 
+    (identified by its PPM value) and all other signals in the NMR spectra. It identifies 
+    significant correlations based on the specified p-value threshold and visualizes 
+    the results in a scatter plot.
+
+    Parameters:
+    -----------
+    spectra : pd.DataFrame
+        A DataFrame containing the NMR spectra data, where each column represents a 
+        chemical shift in ppm and each row represents a sample.
+
+    anchor_ppm_value : float
+        The PPM value of the anchor signal used for correlation analysis.
+
+    p_value_threshold : float, optional
+        The threshold for determining significance. Correlations with a p-value less than 
+        this threshold will be marked as significant. Default is 0.0001.
+
+    Returns:
+    --------
+    fig : go.Figure
+        A Plotly figure object containing the scatter plot of the correlation results.
+
+    Example:
+    ---------
+    >>> fig = STOCSY(spectra=spectra, anchor_ppm_value=1.29275, p_value_threshold=0.0000001)
+    >>> fig.show()
+    """
+    # Step 1: Load NMR spectra data
+
+    ppm = spectra.columns.astype(float).to_list()  # Convert column names to floats (ppm values)
+
+    # Step 2: NMR spectra data (X is already a DataFrame)
+    X = spectra
+
+    # Step 3: Find the index of the anchor ppm in the list of ppm values
+    anchor_index = np.argmin(np.abs(np.array(ppm) - anchor_ppm_value))
+
+    # Step 4: Calculate Pearson correlation and p-values for the anchor point against all others
+    correlations = []
+    p_values = []
+
+    for col in X.columns:
+        # Calculate correlation between the anchor signal and each other signal
+        corr, p_val = pearsonr(X.iloc[:, anchor_index], X[col])
+        correlations.append(corr)
+        p_values.append(p_val)
+
+    correlations = np.array(correlations)
+    p_values = np.array(p_values)
+
+    # Step 5: Calculate r^2 (squared correlation) for each point
+    r_squared = correlations ** 2
+
+    # Step 6: Prepare plotly scatter plot
+    fig = go.Figure()
+
+    # Scatter plot of non-significant points
+    non_significant_mask = p_values >= p_value_threshold
+    fig.add_trace(go.Scatter(
+        x=np.array(ppm)[non_significant_mask],
+        y=X.median()[non_significant_mask],
+        mode='markers',
+        marker=dict(
+            size=3,
+            color='gray',
+        ),
+        name='Non-significant'
+    ))
+
+    # Scatter plot of significant points (marked in red)
+    significant_mask = p_values < p_value_threshold
+    fig.add_trace(go.Scatter(
+        x=np.array(ppm)[significant_mask],
+        y=X.median()[significant_mask],
+        mode='markers',
+        marker=dict(
+            size=3,
+            color='red',  # Red color for significant points
+        ),
+        name=f'Significant (<i>p</i> < {p_value_threshold})'
+    ))
+
+    # Add labels and title
+    fig.update_layout(
+        title={'text':f'<b>STOCSY: δ {np.round(anchor_ppm_value, decimals=4)}</b>',
+                'y':0.9,
+                'x':0.5,
+                'xanchor':'center',
+                'yanchor':'top'},
+        xaxis_title='<b>δ<sup>1</sup>H</b>',
+        yaxis_title=f'Correlation (r<sup>2</sup>) δ = {np.round(anchor_ppm_value, decimals=4)}',
+        showlegend=True
+    )
+
+    #invert x-axis
+    fig.update_xaxes(autorange="reversed")
+    # Display the interactive plot
+    return fig
+
+# Example usage
+#plot_nmr_correlation(spectra=spectra, anchor_ppm_value=1.29275, p_value_threshold=0.0000001)

metbit/__init__.py

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+# -*- coding: utf-8 -*-
+
+from .metbit import opls_da, pca
+from .utility import univar_stats, Normalise
+from .lazy_opls_da import lazy_opls_da
+from .spec_norm import *
+from .peak_processe import peak_chops
+from .STOCSY import STOCSY
+from .ui_stocsy import STOCSY_app
+from .ui_picky_peak import pickie_peak
+from .take_intensity import *
+from .nmr_preprocess import *
+
+
+# -*- coding: utf-8 -*-
+
+__author__ = "aeiwz"
+__email__ = "theerayut_aeiw_123@hotmail.com"
+__maintainer__ = "aeiwz"
+__status__ = "Development"
+__copyright__ = "Copyright 2024, Theerayut"

metbit/base.py

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+# -*- coding: utf-8 -*-
+
+__auther__ ='aeiwz'
+author_email='theerayut_aeiw_123@hotmail.com'
+__copyright__="Copyright 2024, Theerayut"
+
+__license__ = "MIT"
+__maintainer__ = "aeiwz"
+__email__ = "theerayut_aeiw_123@hotmail.com"
+__status__ = "Develop"
+
+import numpy as np
+import numpy.linalg as la
+import typing
+
+
+def nipals(x: np.ndarray, y: np.ndarray,
+           tol: float = 1e-10,
+           max_iter: int = 1000,
+           dot=np.dot) -> typing.Tuple:
+    """
+    Non-linear Iterative Partial Least Squares
+
+    Parameters
+    ----------
+    x: np.ndarray
+        Variable matrix with size n by p, where n number of samples,
+        p number of variables.
+    y: np.ndarray
+        Dependent variable with size n by 1.
+    tol: float
+        Tolerance for the convergence.
+    max_iter: int
+        Maximal number of iterations.
+
+    Returns
+    -------
+    w: np.ndarray
+        Weights with size p by 1.
+    u: np.ndarray
+        Y-scores with size n by 1.
+    c: float
+        Y-weight
+    t: np.ndarray
+        Scores with size n by 1
+
+    References
+    ----------
+    [1] Wold S, et al. PLS-regression: a basic tool of chemometrics.
+        Chemometr Intell Lab Sys 2001, 58, 109–130.
+    [2] Bylesjo M, et al. Model Based Preprocessing and Background
+        Elimination: OSC, OPLS, and O2PLS. in Comprehensive Chemometrics.
+
+    """
+    u = y
+    i = 0
+    d = tol * 10
+    while d > tol and i <= max_iter:
+        w = dot(u, x) / dot(u, u)
+        w /= la.norm(w)
+        t = dot(x, w)
+        c = dot(t, y) / dot(t, t)
+        u_new = y * c / (c * c)
+        d = la.norm(u_new - u) / la.norm(u_new)
+        u = u_new
+        i += 1
+
+    return w, u, c, t