pycodamath 1.1.2__tar.gz → 1.1.4__tar.gz

{pycodamath-1.1.2/src/pycodamath.egg-info → pycodamath-1.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pycodamath
-Version: 1.1.2
+Version: 1.1.4
 Summary: Compositional data (CoDa) analysis tools for Python
 Author-email: Christian Brinch <cbri@food.dtu.dk>
 License: MIT
@@ -285,9 +285,9 @@ The keyword `palette` is a dict mapping each unique group value to a colour.
     import pandas as pd
     data = pd.read_csv('example/kilauea_iki_chem.csv')
     mypca = coda.pca.Biplot(data)
-    mypca.removelabels()
+    mypca.remove("labels")
     mypca.plotloadings(cluster=True)
     print(mypca.clusterlegend)
-    mypca.removelabels()
+    mypca.remove("labels")
     mypca.plotloadings(labels=['FeO', 'Al2O3', 'CaO'], cluster=False)
     mypca.adjustloadinglabels()

{pycodamath-1.1.2 → pycodamath-1.1.4}/README.md

@@ -254,9 +254,9 @@ The keyword `palette` is a dict mapping each unique group value to a colour.
     import pandas as pd
     data = pd.read_csv('example/kilauea_iki_chem.csv')
     mypca = coda.pca.Biplot(data)
-    mypca.removelabels()
+    mypca.remove("labels")
     mypca.plotloadings(cluster=True)
     print(mypca.clusterlegend)
-    mypca.removelabels()
+    mypca.remove("labels")
     mypca.plotloadings(labels=['FeO', 'Al2O3', 'CaO'], cluster=False)
     mypca.adjustloadinglabels()

{pycodamath-1.1.2 → pycodamath-1.1.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pycodamath"
-version = "1.1.2"
+version = "1.1.4"
 authors = [
   { name="Christian Brinch", email="cbri@food.dtu.dk" },
 ]

{pycodamath-1.1.2 → pycodamath-1.1.4}/src/pycodamath/extra.py

@@ -45,9 +45,8 @@ def norm(balances):
 def check_basis(psi):
     ''' Check if basis is orthonormal '''
     ident = psi @ psi.T
-    if np.trace(ident) != ident.shape[0]:
+    if np.abs(np.trace(ident) - ident.shape[0]) > 1e-6:
         raise AttributeError("Error: Basis is not normalized.")
-    #if np.abs(np.sum(ident-np.diag(np.diagonal(ident)))) > 1e-6:
     if np.abs(ident.sum()-np.trace(ident)) > 1e-6:
         raise AttributeError("Error: Basis is not orthogonal.")
 
@@ -83,8 +82,8 @@ def get_covariance_ellipse(data, conf=95):
             ("Error: get_covariance_ellipse expects only two columns. " +
              "Got {0:d}.").format(len(data.columns)))
 
-    lambda_, angle = np.linalg.eig(np.cov(data.loc[:, 0], data.loc[:, 1]))
-    lambda_ = np.sqrt(lambda_)
+    lambda_, angle = np.linalg.eigh(np.cov(data.loc[:, 0], data.loc[:, 1]))
+    lambda_ = np.sqrt(np.maximum(lambda_, 0))
 
     chi2_scales = {90: 4.605, 95: 5.991, 99: 9.210}
     if conf not in chi2_scales:
@@ -93,12 +92,11 @@ def get_covariance_ellipse(data, conf=95):
 
 
     return {'shape': (lambda_[0]*np.sqrt(scale), lambda_[1]*np.sqrt(scale)),
-            # 'angle': np.arccos(-angle[0, 0]),
             'angle': np.arctan(angle[1, 0]/angle[0, 0]),
             'center': (np.mean(data.loc[:, 0]), np.mean(data.loc[:, 1]))}
 
 
-def plot_covariance_ellipse(axis, ellipse, color=0):
+def plot_covariance_ellipse(axis, ellipse, color=None):
     ''' plot covariance ellipse '''
     if color is None:
         color = 'black'

pycodamath-1.1.4/src/pycodamath/pca.py

@@ -0,0 +1,531 @@
+"""Class and methods for making compositional biplots based on PCA"""
+
+__author__ = "Christian Brinch"
+__copyright__ = "Copyright 2019"
+__credits__ = ["Christian Brinch"]
+__license__ = "AFL 3.0"
+__version__ = "1.1"
+__maintainer__ = "Christian Brinch"
+__email__ = "cbri@food.dtu.dk"
+
+import numpy as np
+import matplotlib.pyplot as plt
+import webcolors as wc
+from matplotlib.colors import ListedColormap
+from matplotlib import cm
+from matplotlib.transforms import TransformedBbox
+import matplotlib.patches as mpatches
+import pandas as pd
+import scipy.stats as st
+from scipy.cluster.hierarchy import linkage, cut_tree
+from pycodamath import extra
+
+
+class GeomObj:
+    """A generic container of geometric objects"""
+
+    def __init__(self, **kwargs):
+        vars(self).update(kwargs)
+        self.area = self.polyarea()
+
+    def polyarea(self):
+        """Calculate the area of a polygon given two lists of vertices"""
+        x, y = self.vertices
+        return 0.5 * np.abs(x@np.roll(y,1) - y@np.roll(x,1))
+
+
+def scree_plot(axis, eig_val):
+    """Make scree plot from eigen values"""
+    axis.set_xlabel("Component")
+    axis.set_ylabel("Explained variance")
+    axis.set_xlim(0, min(len(eig_val) + 1, 20))
+    axis.bar(np.arange(len(eig_val)) + 1, (eig_val**2 / np.sum(eig_val** 2)))
+    csum = np.cumsum(eig_val**2 / np.sum(eig_val**2))
+    for i in range(min(5, len(eig_val))):
+        axis.annotate(
+            str(np.round(csum[i] * 100)) + "%",
+            (i + 1.2, (eig_val[i]** 2 / np.sum(eig_val** 2))),
+        )
+
+
+def _get_palette(group):
+    cspace = cm.jet(np.linspace(0, 1, len(set(group))))
+    return {item: cspace[idx] for idx, item in enumerate(set(group))}
+
+
+def _svd(clr):
+    """Internal SVD function"""
+    scores, eig_val, loadings = np.linalg.svd(clr)
+    scores = pd.DataFrame(scores.T[0:2, :], columns=clr.index, index=["pc1", "pc2"])
+    loadings = pd.DataFrame(
+        (eig_val[:,np.newaxis] * loadings)[0:2],
+        columns=clr.columns[0 : len(eig_val)],
+        index=["pc1", "pc2"],
+    )
+    return scores, eig_val, loadings
+
+
+def _bundle_loadings(loadings, threshold=0.05):
+    """Reduce the number of loadings by hierachical clustering"""
+    tree = linkage(loadings.T, "ward")
+    stump = cut_tree(tree, height=tree[-1][2] * threshold)
+    clusters = pd.DataFrame([], index=loadings.index)
+    legend = {}
+    counter = 1
+    stump_flat = np.concatenate(stump)
+    for i in set(stump_flat):
+        features = np.where(stump_flat == i)
+        if len(features[0]) > 1:
+            clusters[counter] = loadings[
+                [loadings.columns[j] for j in features[0]]
+            ].mean(axis=1)
+            legend[counter] = [loadings.columns[j] for j in features[0]]
+            counter += 1
+        else:
+            clusters[loadings.columns[features[0]]] = loadings[
+                loadings.columns[features[0]]
+            ]
+
+    return legend, clusters
+
+
+def _do_bbox_overlap(box1, box2):
+    # If one rectangle is on left side of other
+    return not (
+        box1[1][0] > box2[2][0]
+        or box2[1][0] > box1[2][0]
+        or box1[3][1] > box2[1][1]
+        or box2[2][1] > box1[1][1]
+    )
+
+
+class Biplot:
+    """A class to create and a PCA biplot"""
+
+    def __init__(self, data, axis=None, default=True):
+        if axis is None:
+            _, self.axis = plt.subplots(figsize=(7.8, 7.8))
+        else:
+            self.axis = axis
+        self.axis.set(adjustable="box", aspect="equal")
+        self.scores, eig_val, self.loadings = _svd(
+            data.coda.center().coda.scale().coda.clr()
+        )
+
+        scales = [
+            np.max(np.abs(self.loadings.values)),
+            [np.max(np.abs(self.scores.loc[idx].values)) for idx in ["pc1", "pc2"]],
+        ]
+
+        self.axis.set_xlabel(
+            f"P.C. 1 ({np.round(eig_val[0]**2 / np.sum(eig_val**2)*100):.1f}% explained variation)"
+        )
+        self.axis.set_ylabel(
+            f"P.C. 2 ({np.round(eig_val[1]**2 / np.sum(eig_val**2)*100):.1f}% explained variation)"
+        )
+        self.axis.set_xlim(-scales[0] * 1.1, scales[0] * 1.1)
+        self.axis.set_ylim(-scales[0] * 1.1, scales[0] * 1.1)
+        self.axis.axhline(0, linestyle="--", color="black", alpha=0.4)
+        self.axis.axvline(0, linestyle="--", color="black", alpha=0.4)
+
+        self.scores = (scales[0] * (self.scores.T / scales[1])).T
+
+        self.patches = []
+        self.geomobj = {}
+        plt.tight_layout()
+
+        if default:
+            self.plotloadings()
+            self.plotscores()
+
+    def plotloadings(self, cutoff=0, scale=None, labels=None, cluster=False):
+        """Plot loadings"""
+        if scale is None:
+            scale = np.max(np.abs(self.loadings.values))
+
+        if labels is None:
+            labels = self.loadings.columns
+        loadings = self.loadings[labels]
+
+        if cutoff > 0:
+            length = np.sqrt(loadings.loc["pc1"] ** 2 + loadings.loc["pc2"] ** 2)
+            loadings = loadings.loc[:, length > cutoff * scale]
+
+
+        if cluster:
+            legend, loadings = _bundle_loadings(loadings)
+
+        for column in loadings:
+            self.axis.arrow(
+                0,
+                0,
+                loadings.loc["pc1", column],
+                loadings.loc["pc2", column],
+                facecolor="black",
+                alpha=0.5,
+                linewidth=0.0,
+                width=scale * 0.01,
+                zorder=2000,
+            )
+        self.plotloadinglabels(loadings.columns, loadings, cutoff)
+        if cluster:
+            self.clusterlegend = legend
+
+    def plotloadinglabels(self, labels=None, loadings=None, cutoff=0):
+        """Add labels to the loadings"""
+        if loadings is None:
+            loadings = self.loadings
+        if labels is None:
+            labels = loadings.columns
+
+        fig = self.axis.get_figure()
+        renderer = fig.canvas.get_renderer()
+        for column in labels:
+            if (
+                np.sqrt(
+                    loadings.loc["pc1", column] ** 2 + loadings.loc["pc2", column] ** 2
+                )
+                > cutoff
+            ):
+
+                ann = self.axis.annotate(
+                    str(column)[:30],
+                    (loadings.loc["pc1", column], loadings.loc["pc2", column]),
+                    ha="left",
+                    va="bottom",
+                    alpha=0.95,
+                    color="black",
+                    zorder=5001,
+                )
+
+                fig.canvas.draw()
+                bbox = ann.get_window_extent(renderer=renderer)
+                transform = self.axis.transData.inverted()
+                tbox = TransformedBbox(bbox, transform).corners()
+                if tbox[2][0] > self.axis.get_xlim()[1]:
+                    self.axis.texts[-1]._x -= tbox[2][0] - self.axis.get_xlim()[1]
+                    fig.canvas.draw()
+                    bbox = self.axis.texts[-1].get_window_extent(
+                        renderer=renderer
+                    )
+                    transform = self.axis.transData.inverted()
+                    tbox = TransformedBbox(bbox, transform).corners()
+                    self.axis.texts[-1]._x += self.axis.get_xlim()[1] - tbox[2][0]
+
+    def adjustloadinglabels(self):
+        """Adjust loading label positions, so that labels don't overlap."""
+        fig = self.axis.get_figure()
+        fig.canvas.draw()
+        renderer = fig.canvas.get_renderer()
+        for idx, label in enumerate(self.axis.texts[:-1]):
+            bbox = label.get_window_extent(renderer=renderer)
+            transform = self.axis.transData.inverted()
+            tbox = TransformedBbox(bbox, transform).corners()
+            for tidx, testlabel in enumerate(self.axis.texts[idx + 1 :]):
+                lbox = testlabel.get_window_extent(renderer=renderer)
+                transform = self.axis.transData.inverted()
+                ttbox = TransformedBbox(lbox, transform).corners()
+                if _do_bbox_overlap(tbox, ttbox) or _do_bbox_overlap(ttbox, tbox):
+                    if self.axis.texts[idx]._y < self.axis.texts[idx + tidx + 1]._y:
+                        self.axis.texts[idx]._y -= (tbox[1][1] - tbox[0][1]) / 3.0
+                        self.axis.texts[idx + tidx + 1]._y += (
+                            ttbox[1][1] - ttbox[0][1]
+                        ) / 3.0
+                    else:
+                        self.axis.texts[idx]._y += (tbox[1][1] - tbox[0][1]) / 3.0
+                        self.axis.texts[idx + tidx + 1]._y -= (
+                            ttbox[1][1] - ttbox[0][1]
+                        ) / 3.0
+                    fig.canvas.draw()
+
+    def plotscores(self, group=None, palette=None, legend=True, labels=None):
+        """Plot scores as points"""
+        if labels is None:
+            labels = self.scores.columns
+
+        if palette is None:
+            if group is not None:
+                palette = _get_palette(group)
+            else:
+                palette = "steelblue"
+
+        if group is None:
+            self.axis.plot(
+                *self.scores[labels].values,
+                "o",
+                alpha=0.5,
+                color=palette,
+                zorder=7,
+                markeredgewidth=0,
+            )
+        else:
+            for item in set(group):
+                idx = group.loc[group == item].index
+                self.axis.plot(
+                    *self.scores[idx].values,
+                    "o",
+                    alpha=0.5,
+                    zorder=7,
+                    label=item,
+                    color=palette[item],
+                    markeredgewidth=0,
+                )
+                if legend:
+                    self.patches.append(mpatches.Patch(color=palette[item], label=item))
+
+    def plotscorelabels(self, labels=None):
+        """Add labels to the scores"""
+        if labels is None:
+            labels = self.scores.columns
+
+        for label in labels:
+            self.axis.annotate(
+                label,
+                (self.scores.loc["pc1", label], self.scores.loc["pc2", label]),
+                ha="left",
+                va="bottom",
+                alpha=0.8,
+                zorder=201,
+                size=8,
+            )
+
+    def plotellipses(self, group, palette=None, legend=False):
+        """Plot confidence ellipses"""
+        if palette is None:
+            palette = _get_palette(group)
+
+        for item in set(group):
+            idx = group.loc[group == item].index
+            if len(idx) > 3:
+                ellipse = extra.get_covariance_ellipse(
+                    pd.DataFrame(self.scores[idx].values.T), conf=90
+                )
+                extra.plot_covariance_ellipse(self.axis, ellipse, color=palette[item])
+                if legend:
+                    self.patches.append(mpatches.Patch(color=palette[item], label=item))
+
+    def plotcentroids(self, group, palette=None, legend=False):
+        """Plot score group centroids"""
+        if palette is None:
+            palette = _get_palette(group)
+
+        for item in set(group):
+            idx = group.loc[group == item].index
+            mean_x = self.scores.loc["pc1", idx].mean()
+            mean_y = self.scores.loc["pc2", idx].mean()
+            self.axis.plot(
+                [mean_x],
+                [mean_y],
+                "x",
+                alpha=0.7,
+                label=item,
+                color=palette[item],
+                markersize=24,
+            )
+            if legend:
+                self.patches.append(mpatches.Patch(color=palette[item], label=item))
+
+    def plothulls(self, group, palette=None, legend=True):
+        """Plot score group hulls"""
+        if palette is None:
+            palette = _get_palette(group)
+
+        self.geomobj = {}
+        for item in set(group):
+            idx = group.loc[group == item].index
+            if len(idx) >= 3:
+                # My secret hull construction algorithm
+                idxmin = self.scores.loc["pc1", idx].idxmin()
+                j = self.scores[idx].columns.get_loc(idxmin)
+                hull = [list(self.scores[idxmin])]
+                while j != self.scores[idx].columns.get_loc(idxmin) or len(hull) == 1:
+                    k = (j + 1) % len(idx)
+                    for i in range(len(idx)):
+                        if (
+                            self.scores[idx].iloc[1, k] - self.scores[idx].iloc[1, j]
+                        ) * (
+                            self.scores[idx].iloc[0, i] - self.scores[idx].iloc[0, k]
+                        ) - (
+                            self.scores[idx].iloc[0, k] - self.scores[idx].iloc[0, j]
+                        ) * (
+                            self.scores[idx].iloc[1, i] - self.scores[idx].iloc[1, k]
+                        ) < 0:
+                            k = i
+                    j = k
+                    hull.append(list(self.scores[self.scores[idx].columns[k]]))
+                self.geomobj[item] = GeomObj(vertices=tuple(map(list, zip(*hull))))
+
+        for idx, item in enumerate(
+            sorted(self.geomobj, key=lambda x: self.geomobj[x].area, reverse=True)
+        ):
+            self.axis.fill(
+                *self.geomobj[item].vertices,
+                color=palette[item],
+                alpha=0.7,
+                zorder=10 + (2 * idx),
+            )
+            self.axis.fill(
+                *self.geomobj[item].vertices,
+                facecolor="none",
+                edgecolor="black",
+                alpha=0.9,
+                linewidth=2.2,
+                zorder=11 + (2 * idx),
+            )
+
+            if legend:
+                self.patches.append(mpatches.Patch(color=palette[item], label=item))
+
+    def plotcontours(
+        self,
+        group,
+        palette=None,
+        legend=True,
+        plot_outliers=True,
+        percent_outliers=0.1,
+        linewidth=2.2,
+    ):
+        """Plot scores as contours"""
+        if palette is None and group is not None:
+            palette = _get_palette(group)
+        if percent_outliers > 1 or percent_outliers < 0:
+            raise Exception("Percent_outliers has to be between 0 and 1")
+
+        # Build color maps
+        cmap = {}
+        for item in set(group):
+            colorvalues = np.ones((4, 4))
+            if "#" in str(palette[item]):
+                color = wc.hex_to_rgb(palette[item])
+            elif palette[item][-1] != 1:
+                color = wc.name_to_rgb(palette[item])
+            else:
+                color = palette[item]
+
+            for i in range(3):
+                colorvalues[:, i] = np.linspace(1, color[i] / 256.0, 5)[1:]
+            colorvalues[:, 3] = np.linspace(0.95, 0.25, 4)
+            cmap[item] = ListedColormap(colorvalues)
+
+        self.geomobj = {}
+        for item in set(group):
+            minlevel = 0.2
+            diff = 100
+            k = 0
+            xgrid, ygrid = np.mgrid[
+                self.axis.get_xlim()[0] : self.axis.get_xlim()[1] : 300j,
+                self.axis.get_ylim()[0] : self.axis.get_ylim()[1] : 300j,
+            ]
+            positions = np.vstack([xgrid.ravel(), ygrid.ravel()])
+            while abs(diff) > 0 and k < 25:
+                levels = np.arange(5) * (1.0 - minlevel) / 4.0 + minlevel
+                idx = group.loc[group == item].index
+                values = np.vstack(
+                    [self.scores.loc["pc1", idx], self.scores.loc["pc2", idx]]
+                )
+                kernel = st.gaussian_kde(values)
+                density = np.reshape(kernel(positions).T, xgrid.shape)
+                vals = np.max(density) * levels
+                self.axis.contour(xgrid, ygrid, density, vals)
+                vertices = self.axis.collections[-4].get_paths()[0].vertices.T
+                contained = [False] * len(idx)
+                for j in range(len(self.axis.collections[-5].get_paths())):
+                    contained = np.logical_or(
+                        contained,
+                        self.axis.collections[-5]
+                        .get_paths()[j]
+                        .contains_points(
+                            [
+                                [self.scores.loc["pc1", i], self.scores.loc["pc2", i]]
+                                for i in idx
+                            ]
+                        ),
+                    )
+                _ = [self.axis.collections[-1].remove() for _ in np.arange(5)]
+                outside = [a for a, b in zip(list(idx), contained) if not b]
+
+                diff = round(percent_outliers * len(idx)) - len(outside)
+                minlevel = minlevel + diff / 1000.0
+                k += 1
+
+            self.geomobj[item] = GeomObj(
+                vertices=vertices,
+                grid=(xgrid, ygrid),
+                density=density,
+                values=vals,
+                outside=outside,
+            )
+
+        for idx, item in enumerate(
+            sorted(self.geomobj, key=lambda x: self.geomobj[x].area, reverse=True)
+        ):
+            self.axis.contourf(
+                *self.geomobj[item].grid,
+                self.geomobj[item].density,
+                self.geomobj[item].values,
+                antialiased=True,
+                cmap=cmap[item],
+                alpha=0.9,
+                zorder=10 + (2 * idx),
+            )
+            self.axis.contour(
+                *self.geomobj[item].grid,
+                self.geomobj[item].density,
+                self.geomobj[item].values,
+                antialiased=True,
+                colors="black",
+                alpha=0.5,
+                linewidths=linewidth,
+                zorder=11 + (2 * idx),
+            )
+            self.axis.collections[-1].remove()
+
+            if plot_outliers:
+                self.plotscores(None, palette[item], False, self.geomobj[item].outside)
+
+            if legend:
+                self.patches.append(mpatches.Patch(color=palette[item], label=item))
+
+    def labeloutliers(self, group, conf=3.0):
+        """Print labels on scores that are more than conf away from centroid"""
+        for item in set(group):
+            idx = group.loc[group == item].index
+            length = len(self.scores[idx].T)
+            sum_x = np.sum(self.scores.loc["pc1", idx])
+            sum_y = np.sum(self.scores.loc["pc2", idx])
+
+            mean_x, mean_y = sum_x / length, sum_y / length
+            pdist = {
+                i: np.sqrt(
+                          (self.scores.loc["pc1", i] - mean_x) ** 2
+                          + (self.scores.loc["pc2", i] - mean_y) ** 2
+                      )
+                for i in idx
+            }
+            std = np.std(pdist.values())
+
+            outliers = [i for i in pdist.keys() if pdist[i] > conf * std]
+            self.plotscorelabels(outliers)
+
+    def displaylegend(self, loc=2):
+        """Display the item legend at location loc"""
+        patches = sorted(self.patches, key=lambda x: x._label)
+        for text in self.axis.texts:
+            if (
+                text._x < self.axis.get_xlim()[0] * 1 / 3.0
+                and text._y > self.axis.get_ylim()[1] * 2 / 3.0
+            ):
+                loc += 1
+                break
+        self.axis.legend(handles=patches, fontsize=9, frameon=False, loc=loc)
+
+    def remove(self, item):
+        """ Remove elements from plot """
+        table={"patches":self.axis.patches,
+            "labels": self.axis.texts,
+            "scores": self.axis.lines,
+            "contours": self.axis.collections}
+        if item not in table:
+              raise ValueError(f"Unknown item '{item}'. Choose from: {list(table)}")
+        for _ in range(len(table[item])):
+            table[item][-1].remove()

{pycodamath-1.1.2 → pycodamath-1.1.4}/src/pycodamath/pycoda.py

@@ -5,7 +5,7 @@ __author__ = "Christian Brinch"
 __copyright__ = "Copyright 2019-2026"
 __credits__ = ["Christian Brinch"]
 __license__ = "AFL 3.0"
-__version__ = "1.1.2"
+__version__ = "1.1"
 __maintainer__ = "Christian Brinch"
 __email__ = "cbri@food.dtu.dk"
 

{pycodamath-1.1.2 → pycodamath-1.1.4/src/pycodamath.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pycodamath
-Version: 1.1.2
+Version: 1.1.4
 Summary: Compositional data (CoDa) analysis tools for Python
 Author-email: Christian Brinch <cbri@food.dtu.dk>
 License: MIT
@@ -285,9 +285,9 @@ The keyword `palette` is a dict mapping each unique group value to a colour.
     import pandas as pd
     data = pd.read_csv('example/kilauea_iki_chem.csv')
     mypca = coda.pca.Biplot(data)
-    mypca.removelabels()
+    mypca.remove("labels")
     mypca.plotloadings(cluster=True)
     print(mypca.clusterlegend)
-    mypca.removelabels()
+    mypca.remove("labels")
     mypca.plotloadings(labels=['FeO', 'Al2O3', 'CaO'], cluster=False)
     mypca.adjustloadinglabels()

pycodamath-1.1.2/src/pycodamath/pca.py

@@ -1,456 +0,0 @@
-''' Class and methods for making compositional biplots based on PCA '''
-
-__author__ = "Christian Brinch"
-__copyright__ = "Copyright 2019"
-__credits__ = ["Christian Brinch"]
-__license__ = "AFL 3.0"
-__version__ = "1.1"
-__maintainer__ = "Christian Brinch"
-__email__ = "cbri@food.dtu.dk"
-
-import numpy as np
-import matplotlib.pyplot as plt
-import webcolors as wc
-from matplotlib.colors import ListedColormap
-from matplotlib import cm
-from matplotlib.transforms import TransformedBbox
-import matplotlib.patches as mpatches
-import pandas as pd
-import scipy.stats as st
-from scipy.cluster.hierarchy import linkage, cut_tree
-from pycodamath import extra
-
-
-class GeomObj():
-    ''' A generic container of geometric objects '''
-
-    def __init__(self, **kwargs):
-        vars(self).update(kwargs)
-        self.area = self.polyarea()
-
-    def polyarea(self):
-        ''' Calculate the area of a polygon given two lists of vertices '''
-        x, y = self.vertices
-        return 0.5*np.abs(np.dot(x, np.roll(y, 1))-np.dot(y, np.roll(x, 1)))
-
-
-def scree_plot(axis, eig_val):
-    ''' Make scree plot from eigen values'''
-    axis.set_xlabel('Component')
-    axis.set_ylabel('Explained variance')
-    axis.set_xlim(0, min(len(eig_val)+1, 20))
-    axis.bar(np.arange(len(eig_val))+1, (eig_val/np.sum(eig_val))**2)
-    csum = np.cumsum(eig_val**2/np.sum(eig_val**2))
-    for i in range(min(5, len(eig_val))):
-        axis.annotate(str(np.round(csum[i]*100))+'%',
-                      (i+1.2, (eig_val[i]/np.sum(eig_val))**2))
-
-
-def _get_palette(group):
-    cspace = cm.jet(np.linspace(0, 1, len(set(group))))
-    return {item: cspace[idx] for idx, item in enumerate(set(group))}
-
-
-def _svd(clr):
-    ''' Internal SVD function '''
-    scores, eig_val, loadings = np.linalg.svd(clr)
-    scores = pd.DataFrame(
-        scores.T[0:2, :], columns=clr.index, index=['pc1', 'pc2'])
-    loadings = pd.DataFrame(np.inner(eig_val*np.identity(len(eig_val)),
-                                     loadings.T[0:len(eig_val), 0:len(eig_val)])[0:2],
-                            columns=clr.columns[0:len(eig_val)], index=['pc1', 'pc2'])
-    return scores, eig_val, loadings
-
-
-def _bundle_loadings(loadings, threshold=0.05):
-    ''' Reduce the number of loadings by hierachical clustering '''
-    tree = linkage(loadings.T, 'ward')
-    stump = cut_tree(tree, height=tree[-1][2]*threshold)
-    clusters = pd.DataFrame([], index=loadings.index)
-    legend = {}
-    counter = 1
-    stump_flat = np.concatenate(stump)
-    for i in set(stump_flat):
-        features = np.where(stump_flat == i)
-        if len(features[0]) > 1:
-            clusters[counter] = loadings[[loadings.columns[j]
-                                          for j in features[0]]].mean(axis=1)
-            legend[counter] = [loadings.columns[j] for j in features[0]]
-            counter += 1
-        else:
-            clusters[loadings.columns[features[0]]
-                     ] = loadings[loadings.columns[features[0]]]
-
-    return legend, clusters
-
-
-def _do_bbox_overlap(box1, box2):
-    # If one rectangle is on left side of other
-    return not(box1[1][0] > box2[2][0] or box2[1][0] > box1[2][0]
-        or box1[3][1] > box2[1][1] or box2[2][1] > box1[1][1])
-
-
-class Biplot():
-    ''' A class to create and a PCA biplot '''
-
-    def __init__(self, data, axis=None, default=True):
-        if axis is None:
-            _, self.axis = plt.subplots(figsize=(7.8, 7.8))
-        else:
-            self.axis = axis
-        self.axis.set(adjustable='box', aspect='equal')
-        self.scores, eig_val, self.loadings = _svd(
-            data.coda.center().coda.scale().coda.clr())
-
-        scales = [np.max(np.abs(self.loadings.values)),
-                  [np.max(np.abs(self.scores.loc[idx].values)) for idx in ['pc1', 'pc2']]]
-
-        self.axis.set_xlabel(
-            f'P.C. 1 ({np.round(eig_val[0]**2 / np.sum(eig_val**2)*100):.1f}% explained variation)')
-        self.axis.set_ylabel(
-            f'P.C. 2 ({np.round(eig_val[1]**2 / np.sum(eig_val**2)*100):.1f}% explained variation)')
-        self.axis.set_xlim(-scales[0]*1.1, scales[0]*1.1)
-        self.axis.set_ylim(-scales[0]*1.1, scales[0]*1.1)
-        self.axis.plot([self.axis.get_xlim()[0], self.axis.get_xlim()[1]],
-                       [0.0, 0.0], '--', color='black', alpha=0.4)
-        self.axis.plot([0.0, 0.0], [self.axis.get_ylim()[0], self.axis.get_ylim()[1]],
-                       '--', color='black', alpha=0.4)
-
-        self.scores = (scales[0]*(self.scores.T/scales[1])).T
-
-        self.patches = []
-        self.geomobj = {}
-        plt.tight_layout()
-
-        if default:
-            self.plotloadings()
-            self.plotscores()
-
-    def plotloadings(self, cutoff=0, scale=None, labels=None, cluster=False):
-        ''' Plot loadings '''
-        if scale is None:
-            scale = np.max(np.abs(self.loadings.values))
-
-        if labels is None:
-            labels = self.loadings.columns
-        loadings = self.loadings[labels]
-
-        if cutoff > 0:
-            loadings.loc['len'] = np.sqrt(loadings.loc['pc1']**2 + loadings.loc['pc2']**2)
-            loadings = loadings.T[loadings.T['len'] > cutoff*scale].T
-            loadings = loadings.drop('len')
-
-        if cluster:
-            legend, loadings = _bundle_loadings(loadings)
-
-            # Uncomment this part to print the cluster legend in the figure
-            # x = self.axis.get_xlim()[1]*1.05
-            # y = self.axis.get_ylim()[1]*0.95
-            # for key in legend.keys():
-            #    # plt.text(x, y, str(key)+":", fontsize=10)
-            #    print(str(key)+":", end="")
-            #    for item in legend[key]:
-            #        if len(item) > 22:
-            #            item = item[:22]+'...'
-            #        # plt.text(x, y, "      "+str(item), fontsize=10)
-            #        # y -= (self.axis.get_ylim()[1]-self.axis.get_ylim()[0])/50.
-            #        print("      "+str(item))
-
-        for column in loadings:
-            self.axis.arrow(0, 0,
-                            loadings.loc['pc1', column],
-                            loadings.loc['pc2', column],
-                            facecolor='black',
-                            alpha=0.5,
-                            linewidth=0.,
-                            width=scale*0.01,
-                            zorder=2000)
-        self.plotloadinglabels(loadings.columns, loadings, cutoff)
-        if cluster:
-            self.clusterlegend = legend
-
-    def plotloadinglabels(self, labels=None, loadings=None, cutoff=0):
-        ''' Add labels to the loadings '''
-        if loadings is None:
-            loadings = self.loadings
-        if labels is None:
-            labels = loadings.columns
-
-        for column in labels:
-            if np.sqrt(loadings.loc['pc1', column]**2 +
-                       loadings.loc['pc2', column]**2) > cutoff:
-
-                ann = self.axis.annotate(str(column)[:30], (loadings.loc['pc1', column],
-                                                            loadings.loc['pc2', column]),
-                                         ha='left',
-                                         va='bottom',
-                                         alpha=0.95,
-                                         color='black',
-                                         zorder=5001
-                                         )
-                fig = self.axis.get_figure()
-                fig.canvas.draw()
-                bbox = ann.get_window_extent(
-                    renderer=fig.canvas.get_renderer())
-                transform = self.axis.transData.inverted()
-                tbox = TransformedBbox(bbox, transform).corners()
-                if tbox[2][0] > self.axis.get_xlim()[1]:
-                    self.axis.texts[-1]._x -= (tbox[2]
-                                               [0]-self.axis.get_xlim()[1])
-                    fig.canvas.draw()
-                    bbox = self.axis.texts[-1].get_window_extent(
-                        renderer=fig.canvas.get_renderer())
-                    transform = self.axis.transData.inverted()
-                    tbox = TransformedBbox(bbox, transform).corners()
-                    self.axis.texts[-1]._x += (self.axis.get_xlim()
-                                               [1]-tbox[2][0])
-
-    def adjustloadinglabels(self):
-        ''' Adjust loading label positions, so that labels don't overlap. '''
-        fig = self.axis.get_figure()
-        fig.canvas.draw()
-        for idx, label in enumerate(self.axis.texts[:-1]):
-            bbox = label.get_window_extent(renderer=fig.canvas.get_renderer())
-            transform = self.axis.transData.inverted()
-            tbox = TransformedBbox(bbox, transform).corners()
-            for tidx, testlabel in enumerate(self.axis.texts[idx+1:]):
-                lbox = testlabel.get_window_extent(
-                    renderer=fig.canvas.get_renderer())
-                transform = self.axis.transData.inverted()
-                ttbox = TransformedBbox(lbox, transform).corners()
-                if _do_bbox_overlap(tbox, ttbox) or _do_bbox_overlap(ttbox, tbox):
-                    if self.axis.texts[idx]._y < self.axis.texts[idx+tidx+1]._y:
-                        self.axis.texts[idx]._y -= (tbox[1][1]-tbox[0][1])/3.
-                        self.axis.texts[idx+tidx+1]._y += (ttbox[1]
-                                                           [1]-ttbox[0][1])/3.
-                    else:
-                        self.axis.texts[idx]._y += (tbox[1][1]-tbox[0][1])/3.
-                        self.axis.texts[idx+tidx+1]._y -= (ttbox[1]
-                                                           [1]-ttbox[0][1])/3.
-                    fig.canvas.draw()
-
-    def plotscores(self, group=None, palette=None, legend=True, labels=None):
-        ''' Plot scores as points '''
-        if labels is None:
-            labels = self.scores.columns
-
-        if palette is None:
-            if group is not None:
-                palette = _get_palette(group)
-            else:
-                palette = 'steelblue'
-
-        if group is None:
-            self.axis.plot(*self.scores[labels].values, 'o', alpha=0.5,
-                           color=palette, zorder=7, markeredgewidth=0)
-        else:
-            for item in set(group):
-                idx = group.loc[group == item].index
-                self.axis.plot(*self.scores[idx].values, 'o', alpha=0.5, zorder=7,
-                               label=item, color=palette[item], markeredgewidth=0)
-                if legend:
-                    self.patches.append(mpatches.Patch(
-                        color=palette[item], label=item))
-
-    def plotscorelabels(self, labels=None):
-        ''' Add labels to the scores '''
-        if labels is None:
-            labels = self.scores.columns
-
-        for label in labels:
-            self.axis.annotate(label, (self.scores.loc['pc1', label],
-                                       self.scores.loc['pc2', label]),
-                               ha='left',
-                               va='bottom',
-                               alpha=0.8,
-                               zorder=201,
-                               size=8
-                               )
-
-    def plotellipses(self, group, palette=None, legend=False):
-        ''' Plot confidence ellipses '''
-        if palette is None:
-            palette = _get_palette(group)
-
-        for item in set(group):
-            idx = group.loc[group == item].index
-            if len(idx) > 3:
-                ellipse = extra.get_covariance_ellipse(pd.DataFrame(self.scores[idx].values.T),
-                                                       conf=90)
-                extra.plot_covariance_ellipse(
-                    self.axis, ellipse, color=palette[item])
-                if legend:
-                    self.patches.append(mpatches.Patch(
-                        color=palette[item], label=item))
-
-    def plotcentroids(self, group, palette=None, legend=False):
-        ''' Plot score group centroids '''
-        if palette is None:
-            palette = _get_palette(group)
-
-        for item in set(group):
-            idx = group.loc[group == item].index
-            mean_x = self.scores.loc['pc1', idx].mean()
-            mean_y = self.scores.loc['pc2', idx].mean()
-            self.axis.plot([mean_x], [mean_y], 'x', alpha=0.7,
-                           label=item, color=palette[item], markersize=24)
-            if legend:
-                self.patches.append(mpatches.Patch(
-                    color=palette[item], label=item))
-
-    def plothulls(self, group, palette=None, legend=True):
-        ''' Plot score group hulls '''
-        if palette is None:
-            palette = _get_palette(group)
-
-        self.geomobj = {}
-        for item in set(group):
-            idx = group.loc[group == item].index
-            if len(idx) > 3:
-                # My secret hull construction algorithm
-                idxmin = self.scores.loc['pc1', idx].idxmin()
-                j = self.scores[idx].columns.get_loc(idxmin)
-                hull = [list(self.scores[idxmin])]
-                while (j != self.scores[idx].columns.get_loc(idxmin) or len(hull) == 1):
-                    k = (j + 1) % len(idx)
-                    for i in range(len(idx)):
-                        if (self.scores[idx].iloc[1, k]-self.scores[idx].iloc[1, j]) * \
-                           (self.scores[idx].iloc[0, i]-self.scores[idx].iloc[0, k]) - \
-                           (self.scores[idx].iloc[0, k]-self.scores[idx].iloc[0, j]) * \
-                           (self.scores[idx].iloc[1, i]-self.scores[idx].iloc[1, k]) < 0:
-                            k = i
-                    j = k
-                    hull.append(list(self.scores[self.scores[idx].columns[k]]))
-                self.geomobj[item] = GeomObj(
-                    vertices=tuple(map(list, zip(*hull))))
-
-        for idx, item in enumerate(sorted(self.geomobj,
-                                          key=lambda x: self.geomobj[x].area, reverse=True)):
-            self.axis.fill(*self.geomobj[item].vertices,
-                           color=palette[item], alpha=0.7, zorder=10+(2*idx))
-            self.axis.fill(*self.geomobj[item].vertices, facecolor='none',
-                           edgecolor='black', alpha=0.9, linewidth=2.2, zorder=11+(2*idx))
-
-            if legend:
-                self.patches.append(mpatches.Patch(
-                    color=palette[item], label=item))
-
-    def plotcontours(self, group, palette=None, legend=True,
-                     plot_outliers=True, percent_outliers=0.1, linewidth=2.2):
-        ''' Plot scores as contours '''
-        if palette is None and group is not None:
-            palette = _get_palette(group)
-        if percent_outliers > 1 or percent_outliers < 0:
-            raise Exception('Percent_outliers has to be between 0 and 1')
-
-        # Build color maps
-        cmap = {}
-        for item in set(group):
-            colorvalues = np.ones((4, 4))
-            if '#' in str(palette[item]):
-                color = wc.hex_to_rgb(palette[item])
-            elif palette[item][-1] != 1:
-                color = wc.name_to_rgb(palette[item])
-            else:
-                color = palette[item]
-
-            for i in range(3):
-                colorvalues[:, i] = np.linspace(1, color[i]/256., 5)[1:]
-            colorvalues[:, 3] = np.linspace(.95, .25, 4)
-            cmap[item] = ListedColormap(colorvalues)
-
-        self.geomobj = {}
-        for item in set(group):
-            minlevel = 0.2
-            diff = 100
-            k = 0
-            while abs(diff) > 0 and k < 25:
-                levels = np.arange(5)*(1.-minlevel)/4.+minlevel
-                idx = group.loc[group == item].index
-                xgrid, ygrid = np.mgrid[self.axis.get_xlim()[0]: self.axis.get_xlim()[1]: 300j,
-                                        self.axis.get_ylim()[0]: self.axis.get_ylim()[1]: 300j]
-                positions = np.vstack([xgrid.ravel(), ygrid.ravel()])
-                values = np.vstack(
-                    [self.scores.loc['pc1', idx], self.scores.loc['pc2', idx]])
-                kernel = st.gaussian_kde(values)
-                density = np.reshape(kernel(positions).T, xgrid.shape)
-                vals = np.max(density)*levels
-                self.axis.contour(xgrid, ygrid, density, vals)
-                vertices = self.axis.collections[-4].get_paths()[0].vertices.T
-                contained = [False] * len(idx)
-                for j in range(len(self.axis.collections[-5].get_paths())):
-                    contained = np.logical_or(contained,
-                                              self.axis.collections[-5].get_paths()[j].contains_points(
-                                                  [[self.scores.loc['pc1', i],
-                                                    self.scores.loc['pc2', i]] for i in idx]))
-                _ = [self.axis.collections[-1].remove() for _ in np.arange(5)]
-                outside = [a for a, b in zip(list(idx), contained) if not b]
-
-                diff = round(percent_outliers*len(idx))-len(outside)
-                minlevel = minlevel+diff/1000.
-                k += 1
-
-            self.geomobj[item] = GeomObj(vertices=vertices, grid=(
-                xgrid, ygrid), density=density, values=vals, outside=outside)
-
-        for idx, item in enumerate(sorted(self.geomobj,
-                                          key=lambda x: self.geomobj[x].area, reverse=True)):
-            self.axis.contourf(*self.geomobj[item].grid, self.geomobj[item].density,
-                               self.geomobj[item].values, antialiased=True,
-                               cmap=cmap[item], alpha=0.9, zorder=10+(2*idx))
-            self.axis.contour(*self.geomobj[item].grid, self.geomobj[item].density,
-                              self.geomobj[item].values, antialiased=True,
-                              colors='black', alpha=0.5, linewidths=linewidth, zorder=11+(2*idx))
-            self.axis.collections[-1].remove()
-
-            if plot_outliers:
-                self.plotscores(
-                    None, palette[item], False, self.geomobj[item].outside)
-
-            if legend:
-                self.patches.append(mpatches.Patch(
-                    color=palette[item], label=item))
-
-    def labeloutliers(self, group, conf=3.):
-        ''' Print labels on scores that are more than conf away from centroid '''
-        for item in set(group):
-            idx = group.loc[group == item].index
-            length = len(self.scores[idx].T)
-            sum_x = np.sum(self.scores.loc['pc1', idx])
-            sum_y = np.sum(self.scores.loc['pc2', idx])
-
-            pdist = {i: np.sqrt(self.scores.loc['pc1', i]-sum_x/length**2 +
-                                self.scores.loc['pc2', i]-sum_y/length**2) for i in idx}
-            std = np.std(pdist.values())
-
-            outliers = [i for i in pdist.keys() if pdist[i] > conf*std]
-            self.plotscorelabels(outliers)
-
-    def displaylegend(self, loc=2):
-        ''' Display the item legend at location loc '''
-        patches = sorted(self.patches, key=lambda x: x._label)
-        for text in self.axis.texts:
-            if text._x < self.axis.get_xlim()[0]*1/3. and text._y > self.axis.get_ylim()[1]*2/3.:
-                loc += 1
-                break
-        self.axis.legend(handles=patches, fontsize=9, frameon=False, loc=loc)
-
-    def removepatches(self):
-        ''' remove arrows and polygons from plot '''
-        for _ in range(len(self.axis.patches)):
-            self.axis.patches[-1].remove()
-
-    def removelabels(self):
-        ''' remove labels from plot '''
-        for _ in range(len(self.axis.texts)):
-            self.axis.texts[-1].remove()
-
-    def removescores(self):
-        ''' remove points from plot '''
-        for _ in range(len(self.axis.lines)):
-            self.axis.lines[-1].remove()
-
-    def removecontours(self):
-        ''' remove points from plot '''
-        for _ in range(len(self.axis.collections)):
-            self.axis.collections[-1].remove()