msreport 0.0.27__py3-none-any.whl → 0.0.29__py3-none-any.whl

msreport/plot/distribution.py

@@ -0,0 +1,253 @@
+import itertools
+import warnings
+from collections.abc import Iterable, Sequence
+from typing import Optional
+
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import seaborn as sns
+
+from msreport.qtable import Qtable
+
+from .style import ColorWheelDict, with_active_style
+
+
+@with_active_style
+def replicate_ratios(
+    qtable: Qtable,
+    exclude_invalid: bool = True,
+    xlim: Iterable[float] = (-2, 2),
+) -> tuple[plt.Figure, list[plt.Axes]]:
+    """Figure to compare the similarity of expression values between replicates.
+
+    Displays the distribution of pair-wise log2 ratios between samples of the same
+    experiment. Comparisons of the same experiment are placed in the same row. Requires
+    log2 transformed expression values.
+
+    Args:
+        qtable: A `Qtable` instance, which data is used for plotting.
+        exclude_invalid: If True, rows are filtered according to the Boolean entries of
+            the "Valid" column.
+        xlim: Specifies the displayed range for the log2 ratios on the x-axis. Default
+            is from -2 to 2.
+
+    Returns:
+        A matplotlib Figure and a list of Axes objects, containing the comparison plots.
+    """
+    tag: str = "Expression"
+    table = qtable.make_sample_table(
+        tag, samples_as_columns=True, exclude_invalid=exclude_invalid
+    )
+    design = qtable.get_design()
+
+    color_wheel = ColorWheelDict()
+    for exp in design["Experiment"].unique():
+        _ = color_wheel[exp]
+
+    experiments = []
+    for experiment in design["Experiment"].unique():
+        if len(qtable.get_samples(experiment)) >= 2:
+            experiments.append(experiment)
+    if not experiments:
+        fig, ax = plt.subplots(1, 1, figsize=(2, 1.3))
+        fig.suptitle("Pair wise comparison of replicates", y=1.1)
+        ax.text(0.5, 0.5, "No replicate\ndata available", ha="center", va="center")
+        ax.grid(False)
+        ax.tick_params(left=False, bottom=False, labelleft=False, labelbottom=False)
+        sns.despine(top=False, right=False, fig=fig)
+        return fig, np.array([ax])
+
+    num_experiments = len(experiments)
+    max_replicates = max([len(qtable.get_samples(exp)) for exp in experiments])
+    max_combinations = len(list(itertools.combinations(range(max_replicates), 2)))
+
+    suptitle_space_inch = 0.55
+    ax_height_inch = 0.6
+    ax_width_inch = 1.55
+    ax_hspace_inch = 0.35
+    fig_height = (
+        num_experiments * ax_height_inch
+        + (num_experiments - 1) * ax_hspace_inch
+        + suptitle_space_inch
+    )
+    fig_width = max_combinations * ax_width_inch
+    fig_size = (fig_width, fig_height)
+
+    subplot_top = 1 - (suptitle_space_inch / fig_height)
+    subplot_hspace = ax_hspace_inch / ax_height_inch
+
+    fig, axes = plt.subplots(
+        num_experiments, max_combinations, figsize=fig_size, sharex=True
+    )
+    if num_experiments == 1 and max_combinations == 1:
+        axes = np.array([[axes]])
+    elif num_experiments == 1:
+        axes = np.array([axes])
+    elif max_combinations == 1:
+        axes = np.array([axes]).T
+    fig.subplots_adjust(
+        bottom=0, top=subplot_top, left=0, right=1, hspace=subplot_hspace
+    )
+    fig.suptitle("Pair wise comparison of replicates", y=1)
+
+    for x_pos, experiment in enumerate(experiments):
+        sample_combinations = itertools.combinations(qtable.get_samples(experiment), 2)
+        for y_pos, (s1, s2) in enumerate(sample_combinations):
+            s1_label = design.loc[(design["Sample"] == s1), "Replicate"].tolist()[0]
+            s2_label = design.loc[(design["Sample"] == s2), "Replicate"].tolist()[0]
+            ax = axes[x_pos, y_pos]
+            ratios = table[s1] - table[s2]
+            ratios = ratios[np.isfinite(ratios)]
+            ylabel = experiment if y_pos == 0 else ""
+            title = f"{s1_label} vs {s2_label}"
+            color = color_wheel[experiment]
+
+            sns.kdeplot(x=ratios, fill=True, ax=ax, zorder=3, color=color, alpha=0.5)
+            ax.set_title(title, fontsize=plt.rcParams["axes.labelsize"])
+            ax.set_ylabel(ylabel, rotation=0, va="center", ha="right")
+            ax.set_xlabel("Ratio [log2]")
+            ax.tick_params(labelleft=False)
+            ax.locator_params(axis="x", nbins=5)
+
+    axes[0, 0].set_xlim(xlim)
+    for ax in axes.flatten():
+        if not ax.has_data():
+            ax.remove()
+            continue
+
+        ax.axvline(x=0, color="#999999", lw=1, zorder=2)
+        ax.grid(False, axis="y")
+    sns.despine(top=True, right=True, fig=fig)
+
+    return fig, axes
+
+
+@with_active_style
+def experiment_ratios(
+    qtable: Qtable,
+    experiments: Optional[str] = None,
+    exclude_invalid: bool = True,
+    ylim: Sequence[float] = (-2, 2),
+) -> tuple[plt.Figure, list[plt.Axes]]:
+    """Figure to compare the similarity of expression values between experiments.
+
+    Intended to evaluate the bulk distribution of expression values after normalization.
+    For each experiment a subplot is generated, which displays the distribution of log2
+    ratios to a pseudo reference experiment as a density plot. The pseudo reference
+    values are calculated as the average intensity values of all experiments. Only rows
+    with quantitative values in all experiment are considered.
+
+    Requires "Events experiment" columns and that average experiment expression values
+    are calculated. This can be achieved by calling
+    `msreport.analyze.analyze_missingness(qtable: Qtable)` and
+    `msreport.analyze.calculate_experiment_means(qtable: Qtable)`.
+
+    Args:
+        qtable: A `Qtable` instance, which data is used for plotting.
+        experiments: Optional, list of experiments that will be displayed. If None, all
+            experiments from `qtable.design` will be used.
+        exclude_invalid: If True, rows are filtered according to the Boolean entries of
+            the "Valid" column.
+        ylim: Specifies the displayed range for the log2 ratios on the y-axis. Default
+            is from -2 to 2.
+
+    Raises:
+        ValueError: If only one experiment is specified in the `experiments` parameter
+            or if the specified experiments are not present in the qtable design.
+
+    Returns:
+        A matplotlib Figure and a list of Axes objects, containing the comparison plots.
+    """
+    tag: str = "Expression"
+
+    if experiments is not None and len(experiments) == 1:
+        raise ValueError(
+            "Only one experiment is specified, please provide at least two experiments."
+        )
+    elif experiments is not None:
+        experiments_not_in_design = set(experiments) - set(qtable.design["Experiment"])
+        if experiments_not_in_design:
+            raise ValueError(
+                "All experiments must be present in qtable.design. The following "
+                f"experiments are not present: {experiments_not_in_design}"
+            )
+    else:
+        experiments = qtable.design["Experiment"].unique().tolist()
+
+    if len(experiments) < 2:
+        fig, ax = plt.subplots(1, 1, figsize=(2.5, 1.3))
+        fig.suptitle("Comparison of experiments means", y=1.1)
+        ax.text(
+            0.5,
+            0.5,
+            "Comparison not possible.\nOnly one experiment\npresent in design.",
+            ha="center",
+            va="center",
+        )
+        ax.grid(False)
+        ax.tick_params(left=False, bottom=False, labelleft=False, labelbottom=False)
+        sns.despine(top=False, right=False, fig=fig)
+        return fig, np.array([ax])
+
+    sample_data = qtable.make_sample_table(tag, samples_as_columns=True)
+    experiment_means = {}
+    for experiment in experiments:
+        samples = qtable.get_samples(experiment)
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", category=RuntimeWarning)
+            row_means = np.nanmean(sample_data[samples], axis=1)
+        experiment_means[experiment] = row_means
+    experiment_data = pd.DataFrame(experiment_means)
+
+    # Only consider rows with quantitative values in all experiments
+    mask = np.all([(qtable.data[f"Events {exp}"] > 0) for exp in experiments], axis=0)
+    if exclude_invalid:
+        mask = mask & qtable["Valid"]
+    experiment_data = experiment_data[mask]
+    pseudo_reference = np.nanmean(experiment_data, axis=1)
+    ratio_data = experiment_data.subtract(pseudo_reference, axis=0)
+
+    color_wheel = ColorWheelDict()
+    for exp in qtable.design["Experiment"].unique():
+        _ = color_wheel[exp]
+    num_experiments = len(experiments)
+
+    suptitle_space_inch = 0.55
+    ax_height_inch = 1.25
+    ax_width_inch = 0.65
+    ax_wspace_inch = 0.2
+    fig_height = ax_height_inch + suptitle_space_inch
+    fig_width = num_experiments * ax_width_inch + (num_experiments - 1) * ax_wspace_inch
+    fig_size = (fig_width, fig_height)
+
+    subplot_top = 1 - (suptitle_space_inch / fig_height)
+    subplot_wspace = ax_wspace_inch / ax_width_inch
+
+    fig, axes = plt.subplots(1, num_experiments, figsize=fig_size, sharey=True)
+    fig.subplots_adjust(
+        bottom=0, top=subplot_top, left=0, right=1, wspace=subplot_wspace
+    )
+    fig.suptitle("Comparison of experiments means", y=1)
+
+    for exp_pos, experiment in enumerate(experiments):
+        ax = axes[exp_pos]
+        values = ratio_data[experiment]
+        color = color_wheel[experiment]
+        sns.kdeplot(y=values, fill=True, ax=ax, zorder=3, color=color, alpha=0.5)
+        if exp_pos == 0:
+            ax.set_title(
+                f"n={str(len(values))}",
+                fontsize=plt.rcParams["xtick.labelsize"],
+                loc="left",
+            )
+        ax.tick_params(labelbottom=False)
+        ax.set_xlabel(experiment, rotation=90)
+
+    axes[0].set_ylabel("Ratio [log2]\nto pseudo reference")
+    axes[0].set_ylim(ylim)
+    for ax in axes:
+        ax.axhline(y=0, color="#999999", lw=1, zorder=2)
+        ax.grid(False, axis="x")
+    sns.despine(top=True, right=True, fig=fig)
+    return fig, axes

msreport/plot/multivariate.py

@@ -0,0 +1,355 @@
+from typing import Any
+
+import adjustText
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import seaborn as sns
+import sklearn.decomposition
+import sklearn.preprocessing
+
+import msreport.helper
+from msreport.qtable import Qtable
+
+from .style import ColorWheelDict, with_active_style
+
+
+@with_active_style
+def sample_pca(
+    qtable: Qtable,
+    tag: str = "Expression",
+    pc_x: str = "PC1",
+    pc_y: str = "PC2",
+    exclude_invalid: bool = True,
+) -> tuple[plt.Figure, list[plt.Axes]]:
+    """Figure to compare sample similarities with a principle component analysis.
+
+    On the left subplots two PCA components of log2 transformed, mean centered intensity
+    values are shown. On the right subplot the explained variance of the principle
+    components is display as barplots.
+
+    It is possible to use intensity columns that are either log-transformed or not. The
+    intensity values undergo an automatic evaluation to determine if they are already
+    in log-space, and if necessary, they are transformed accordingly.
+
+    Args:
+        qtable: A `Qtable` instance, which data is used for plotting.
+        tag: A string that is used to extract intensity containing columns.
+            Default "Expression".
+        pc_x: Principle component to plot on x-axis of the scatter plot, default "PC1".
+            The number of calculated principal components is equal to the number of
+            samples.
+        pc_y: Principle component to plot on y-axis of the scatter plot, default "PC2".
+            The number of calculated principal components is equal to the number of
+            samples.
+        exclude_invalid: If True, rows are filtered according to the Boolean entries of
+            the "Valid" column.
+
+    Returns:
+        A matplotlib Figure and a list of Axes objects, containing the PCA plots.
+    """
+    design = qtable.get_design()
+    if design.shape[0] < 3:
+        fig, ax = plt.subplots(1, 1, figsize=(2, 1.3))
+        fig.suptitle(f'PCA of "{tag}" values', y=1.1)
+        ax.text(
+            0.5,
+            0.5,
+            "PCA analysis cannot\nbe performed with\nless than 3 samples",
+            ha="center",
+            va="center",
+        )
+        ax.grid(False)
+        ax.tick_params(left=False, bottom=False, labelleft=False, labelbottom=False)
+        sns.despine(top=True, right=True, fig=fig)
+        return fig, np.array([ax])
+
+    table = qtable.make_sample_table(
+        tag, samples_as_columns=True, exclude_invalid=exclude_invalid
+    )
+    table = table.replace({0: np.nan})
+    table = table[np.isfinite(table).sum(axis=1) > 0]
+    if not msreport.helper.intensities_in_logspace(table):
+        table = np.log2(table)
+    table[table.isna()] = 0
+
+    table = table.transpose()
+    sample_index = table.index.tolist()
+    table = sklearn.preprocessing.scale(table, with_std=False)
+
+    num_components = min(len(sample_index) - 1, 9)
+    pca = sklearn.decomposition.PCA(n_components=num_components)
+    components = pca.fit_transform(table)
+    component_labels = ["PC{}".format(i + 1) for i in range(components.shape[1])]
+    components_table = pd.DataFrame(
+        data=components, columns=component_labels, index=sample_index
+    )
+    variance = pca.explained_variance_ratio_ * 100
+    variance_lookup = dict(zip(component_labels, variance, strict=True))
+
+    # Prepare colors
+    color_wheel = ColorWheelDict()
+    for exp in qtable.get_experiments():
+        _ = color_wheel[exp]
+
+    # Prepare figure
+    num_legend_cols = 3  # math.ceil(len(qtable.get_experiments()) / 8)
+    bar_width = 0.8
+    bar_width_inches = 0.25
+    x_padding = 0.25
+
+    suptitle_space_inch = 0.4
+    ax_height_inch = 2.7
+    ax_width_inch = ax_height_inch
+    ax_wspace_inch = 0.6
+    bar_ax_width_inch = (num_components + (2 * x_padding)) * bar_width_inches
+    width_ratios = [ax_width_inch, bar_ax_width_inch]
+
+    fig_height = suptitle_space_inch + ax_height_inch
+    fig_width = ax_height_inch + bar_ax_width_inch + ax_wspace_inch
+    fig_size = (fig_width, fig_height)
+
+    subplot_top = 1 - (suptitle_space_inch / fig_height)
+    subplot_wspace = ax_wspace_inch / np.mean([ax_width_inch, bar_ax_width_inch])
+
+    bar_half_width = 0.5
+    lower_xbound = (0 - bar_half_width) - x_padding
+    upper_xbound = (num_components - 1) + bar_half_width + x_padding
+
+    fig, axes = plt.subplots(
+        1,
+        2,
+        figsize=fig_size,
+        gridspec_kw={
+            "bottom": 0,
+            "top": subplot_top,
+            "left": 0,
+            "right": 1,
+            "wspace": subplot_wspace,
+            "width_ratios": width_ratios,
+        },
+    )
+    fig.suptitle(f'PCA of "{tag}" values', y=1)
+
+    # Comparison of two principle components
+    ax = axes[0]
+    texts = []
+    for sample, data in components_table.iterrows():
+        experiment = qtable.get_experiment(str(sample))
+        label = design.loc[(design["Sample"] == sample), "Replicate"].tolist()[0]
+        color = color_wheel[experiment]
+        edge_color = color_wheel.modified_color(experiment, 0.4)
+        ax.scatter(
+            data[pc_x],
+            data[pc_y],
+            color=color,
+            edgecolor=edge_color,
+            lw=0.7,
+            s=50,
+            label=experiment,
+        )
+        texts.append(ax.text(data[pc_x], data[pc_y], label))
+    adjustText.adjust_text(
+        texts,
+        force_text=0.15,
+        expand_points=(1.4, 1.4),
+        lim=20,
+        ax=ax,
+    )
+    ax.set_xlabel(f"{pc_x} ({variance_lookup[pc_x]:.1f}%)")
+    ax.set_ylabel(f"{pc_y} ({variance_lookup[pc_y]:.1f}%)")
+    ax.grid(axis="both", linestyle="dotted")
+
+    # Explained variance bar plot
+    ax = axes[1]
+    xpos = range(len(variance))
+    ax.bar(xpos, variance, width=bar_width, color="#D0D0D0", edgecolor="#000000")
+    ax.set_xticks(xpos)
+    ax.set_xticklabels(
+        component_labels,
+        rotation="vertical",
+        ha="center",
+        size=plt.rcParams["axes.labelsize"],
+    )
+    ax.set_ylabel("Explained variance [%]")
+    ax.grid(False, axis="x")
+    ax.set_xlim(lower_xbound, upper_xbound)
+
+    handles, labels = axes[0].get_legend_handles_labels()
+    experiment_handles = dict(zip(labels, handles, strict=True))
+
+    first_ax_bbox = axes[1].get_position()
+    legend_xgap_inches = 0.25
+    legend_ygap_inches = 0.03
+    legend_bbox_x = first_ax_bbox.x1 + (legend_xgap_inches / fig.get_figwidth())
+    legend_bbox_y = first_ax_bbox.y1 + (legend_ygap_inches / fig.get_figheight())
+    handles, _ = axes[0].get_legend_handles_labels()
+    num_legend_cols = np.ceil(len(qtable.get_experiments()) / 12)
+    fig.legend(
+        handles=experiment_handles.values(),
+        loc="upper left",
+        bbox_to_anchor=(legend_bbox_x, legend_bbox_y),
+        title="Experiment",
+        alignment="left",
+        frameon=False,
+        borderaxespad=0,
+        ncol=num_legend_cols,
+    )
+
+    return fig, axes
+
+
+@with_active_style
+def expression_clustermap(
+    qtable: Qtable,
+    exclude_invalid: bool = True,
+    remove_imputation: bool = True,
+    mean_center: bool = False,
+    cluster_samples: bool = True,
+    cluster_method: str = "average",
+) -> sns.matrix.ClusterGrid:
+    """Plot sample expression values as a hierarchically-clustered heatmap.
+
+    By default missing and imputed values are assigned an intensity value of 0 to
+    perform the clustering. Once clustering is done, these values are removed from the
+    heatmap, making them appear white.
+
+    Args:
+        qtable: A `Qtable` instance, which data is used for plotting.
+        exclude_invalid: If True, rows are filtered according to the Boolean entries of
+            the "Valid" column.
+        remove_imputation: If True, imputed values are set to 0 before clustering.
+            Defaults to True.
+        mean_center: If True, the data is mean-centered before clustering. Defaults to
+            False.
+        cluster_samples: If True, sample order is determined by hierarchical clustering.
+            Otherwise, the order is determined by the order of samples in the qtable
+            design. Defaults to True.
+        cluster_method: Linkage method to use for calculating clusters. See
+            `scipy.cluster.hierarchy.linkage` documentation for more information.
+
+    Raises:
+        ValueError: If less than two samples are present in the qtable.
+
+    Returns:
+        A seaborn ClusterGrid instance. Note that ClusterGrid has a `savefig` method
+        that can be used for saving the figure.
+    """
+    tag: str = "Expression"
+    samples = qtable.get_samples()
+    experiments = qtable.get_experiments()
+
+    if len(samples) < 2:
+        raise ValueError("At least two samples are required to generate a clustermap.")
+
+    data = qtable.make_expression_table(samples_as_columns=True)
+    data = data[samples]
+
+    for sample in samples:
+        if remove_imputation:
+            data.loc[qtable.data[f"Missing {sample}"], sample] = 0
+        data[sample] = data[sample].fillna(0)
+
+    if not mean_center:
+        # Hide missing values in the heatmap, making them appear white
+        mask_values = qtable.data[
+            [f"Missing {sample}" for sample in samples]
+        ].to_numpy()
+    else:
+        mask_values = np.zeros(data.shape, dtype=bool)
+
+    if exclude_invalid:
+        data = data[qtable.data["Valid"]]
+        mask_values = mask_values[qtable.data["Valid"]]
+
+    color_wheel = ColorWheelDict()
+    for exp in experiments:
+        _ = color_wheel[exp]
+    sample_colors = [color_wheel[qtable.get_experiment(sample)] for sample in samples]
+
+    suptitle_space_inch = 0.4
+    sample_width_inch = 0.27
+    cbar_height_inch = 3
+    cbar_width_inch = sample_width_inch
+    cbar_gap_inch = sample_width_inch
+    col_colors_height_inch = 0.12
+    col_dendrogram_height_inch = 0.6 if cluster_samples else 0.0
+    heatmap_height_inch = 3
+    heatmap_width_inch = len(samples) * sample_width_inch
+
+    fig_width = cbar_width_inch + heatmap_width_inch + cbar_gap_inch
+    fig_height = (
+        suptitle_space_inch
+        + col_dendrogram_height_inch
+        + col_colors_height_inch
+        + heatmap_height_inch
+    )
+    fig_size = fig_width, fig_height
+
+    heatmap_width = heatmap_width_inch / fig_width
+    heatmap_x0 = 0
+    heatmap_height = heatmap_height_inch / fig_height
+    heatmap_y0 = 0
+    col_colors_height = col_colors_height_inch / fig_height
+    col_colors_y0 = heatmap_y0 + heatmap_height
+    col_dendrogram_height = col_dendrogram_height_inch / fig_height
+    col_dendrogram_y0 = col_colors_y0 + col_colors_height
+    cbar_widh = cbar_width_inch / fig_width
+    cbar_x0 = (heatmap_width_inch + cbar_gap_inch) / fig_width
+    cbar_height = cbar_height_inch / fig_height
+    cbar_y0 = col_colors_y0 - cbar_height
+
+    heatmap_args: dict[str, Any] = {
+        "cmap": "magma",
+        "yticklabels": False,
+        "figsize": fig_size,
+    }
+    if mean_center:
+        data = data.sub(data.mean(axis=1), axis=0)
+        heatmap_args.update({"vmin": -2.5, "vmax": 2.5, "center": 0, "cmap": "vlag"})
+
+    # Generate the plot
+    grid = sns.clustermap(
+        data,
+        col_cluster=cluster_samples,
+        col_colors=sample_colors,
+        row_colors=["#000000" for _ in range(len(data))],
+        mask=mask_values,
+        method=cluster_method,
+        metric="euclidean",
+        **heatmap_args,
+    )
+    # Reloacte clustermap axes to create a consistent layout
+    grid.figure.suptitle(f'Hierarchically-clustered heatmap of "{tag}" values', y=1)
+    grid.figure.delaxes(grid.ax_row_colors)
+    grid.figure.delaxes(grid.ax_row_dendrogram)
+    grid.ax_heatmap.set_position(
+        [heatmap_x0, heatmap_y0, heatmap_width, heatmap_height]
+    )
+    grid.ax_col_colors.set_position(
+        [heatmap_x0, col_colors_y0, heatmap_width, col_colors_height]
+    )
+    grid.ax_col_dendrogram.set_position(
+        [heatmap_x0, col_dendrogram_y0, heatmap_width, col_dendrogram_height]
+    )
+    grid.ax_cbar.set_position([cbar_x0, cbar_y0, cbar_widh, cbar_height])
+
+    # manually set xticks to guarantee that all samples are displayed
+    if cluster_samples:
+        sample_order = [samples[i] for i in grid.dendrogram_col.reordered_ind]
+    else:
+        sample_order = samples
+    sample_ticks = np.arange(len(sample_order)) + 0.5
+    grid.ax_heatmap.grid(False)
+    grid.ax_heatmap.set_xticks(sample_ticks, labels=sample_order)
+    grid.ax_heatmap.tick_params(
+        axis="x", labelsize=plt.rcParams["axes.labelsize"], rotation=90
+    )
+
+    grid.ax_heatmap.set_facecolor("#F9F9F9")
+
+    for ax in [grid.ax_heatmap, grid.ax_cbar, grid.ax_col_colors]:
+        sns.despine(top=False, right=False, left=False, bottom=False, ax=ax)
+        for spine in ["top", "right", "left", "bottom"]:
+            ax.spines[spine].set_linewidth(0.75)
+    return grid