.. note:: :class: sphx-glr-download-link-note Click :ref:`here ` to download the full example code .. rst-class:: sphx-glr-example-title .. _sphx_glr_gallery_images_contours_and_fields_image_annotated_heatmap.py: =========================== Creating annotated heatmaps =========================== It is often desirable to show data which depends on two independent variables as a color coded image plot. This is often referred to as a heatmap. If the data is categorical, this would be called a categorical heatmap. Matplotlib's :meth:`imshow ` function makes production of such plots particularly easy. The following examples show how to create a heatmap with annotations. We will start with an easy example and expand it to be usable as a universal function. A simple categorical heatmap ---------------------------- We may start by defining some data. What we need is a 2D list or array which defines the data to color code. We then also need two lists or arrays of categories; of course the number of elements in those lists need to match the data along the respective axes. The heatmap itself is an :meth:`imshow ` plot with the labels set to the categories we have. Note that it is important to set both, the tick locations (:meth:`set_xticks`) as well as the tick labels (:meth:`set_xticklabels`), otherwise they would become out of sync. The locations are just the ascending integer numbers, while the ticklabels are the labels to show. Finally we can label the data itself by creating a :class:`~matplotlib.text.Text` within each cell showing the value of that cell. .. code-block:: python import numpy as np import matplotlib import matplotlib.pyplot as plt # sphinx_gallery_thumbnail_number = 2 vegetables = ["cucumber", "tomato", "lettuce", "asparagus", "potato", "wheat", "barley"] farmers = ["Farmer Joe", "Upland Bros.", "Smith Gardening", "Agrifun", "Organiculture", "BioGoods Ltd.", "Cornylee Corp."] harvest = np.array([[0.8, 2.4, 2.5, 3.9, 0.0, 4.0, 0.0], [2.4, 0.0, 4.0, 1.0, 2.7, 0.0, 0.0], [1.1, 2.4, 0.8, 4.3, 1.9, 4.4, 0.0], [0.6, 0.0, 0.3, 0.0, 3.1, 0.0, 0.0], [0.7, 1.7, 0.6, 2.6, 2.2, 6.2, 0.0], [1.3, 1.2, 0.0, 0.0, 0.0, 3.2, 5.1], [0.1, 2.0, 0.0, 1.4, 0.0, 1.9, 6.3]]) fig, ax = plt.subplots() im = ax.imshow(harvest) # We want to show all ticks... ax.set_xticks(np.arange(len(farmers))) ax.set_yticks(np.arange(len(vegetables))) # ... and label them with the respective list entries ax.set_xticklabels(farmers) ax.set_yticklabels(vegetables) # Rotate the tick labels and set their alignment. plt.setp(ax.get_xticklabels(), rotation=45, ha="right", rotation_mode="anchor") # Loop over data dimensions and create text annotations. for i in range(len(vegetables)): for j in range(len(farmers)): text = ax.text(j, i, harvest[i, j], ha="center", va="center", color="w") ax.set_title("Harvest of local farmers (in tons/year)") fig.tight_layout() plt.show() .. image:: /gallery/images_contours_and_fields/images/sphx_glr_image_annotated_heatmap_001.png :class: sphx-glr-single-img Using the helper function code style ------------------------------------ As discussed in the :ref:`Coding styles ` one might want to reuse such code to create some kind of heatmap for different input data and/or on different axes. We create a function that takes the data and the row and column labels as input, and allows arguments that are used to customize the plot Here, in addition to the above we also want to create a colorbar and position the labels above of the heatmap instead of below it. The annotations shall get different colors depending on a threshold for better contrast against the pixel color. Finally, we turn the surrounding axes spines off and create a grid of white lines to separate the cells. .. code-block:: python def heatmap(data, row_labels, col_labels, ax=None, cbar_kw={}, cbarlabel="", **kwargs): """ Create a heatmap from a numpy array and two lists of labels. Arguments: data : A 2D numpy array of shape (N,M) row_labels : A list or array of length N with the labels for the rows col_labels : A list or array of length M with the labels for the columns Optional arguments: ax : A matplotlib.axes.Axes instance to which the heatmap is plotted. If not provided, use current axes or create a new one. cbar_kw : A dictionary with arguments to :meth:`matplotlib.Figure.colorbar`. cbarlabel : The label for the colorbar All other arguments are directly passed on to the imshow call. """ if not ax: ax = plt.gca() # Plot the heatmap im = ax.imshow(data, **kwargs) # Create colorbar cbar = ax.figure.colorbar(im, ax=ax, **cbar_kw) cbar.ax.set_ylabel(cbarlabel, rotation=-90, va="bottom") # We want to show all ticks... ax.set_xticks(np.arange(data.shape[1])) ax.set_yticks(np.arange(data.shape[0])) # ... and label them with the respective list entries. ax.set_xticklabels(col_labels) ax.set_yticklabels(row_labels) # Let the horizontal axes labeling appear on top. ax.tick_params(top=True, bottom=False, labeltop=True, labelbottom=False) # Rotate the tick labels and set their alignment. plt.setp(ax.get_xticklabels(), rotation=-30, ha="right", rotation_mode="anchor") # Turn spines off and create white grid. for edge, spine in ax.spines.items(): spine.set_visible(False) ax.set_xticks(np.arange(data.shape[1]+1)-.5, minor=True) ax.set_yticks(np.arange(data.shape[0]+1)-.5, minor=True) ax.grid(which="minor", color="w", linestyle='-', linewidth=3) ax.tick_params(which="minor", bottom=False, left=False) return im, cbar def annotate_heatmap(im, data=None, valfmt="{x:.2f}", textcolors=["black", "white"], threshold=None, **textkw): """ A function to annotate a heatmap. Arguments: im : The AxesImage to be labeled. Optional arguments: data : Data used to annotate. If None, the image's data is used. valfmt : The format of the annotations inside the heatmap. This should either use the string format method, e.g. "$ {x:.2f}", or be a :class:`matplotlib.ticker.Formatter`. textcolors : A list or array of two color specifications. The first is used for values below a threshold, the second for those above. threshold : Value in data units according to which the colors from textcolors are applied. If None (the default) uses the middle of the colormap as separation. Further arguments are passed on to the created text labels. """ if not isinstance(data, (list, np.ndarray)): data = im.get_array() # Normalize the threshold to the images color range. if threshold is not None: threshold = im.norm(threshold) else: threshold = im.norm(data.max())/2. # Set default alignment to center, but allow it to be # overwritten by textkw. kw = dict(horizontalalignment="center", verticalalignment="center") kw.update(textkw) # Get the formatter in case a string is supplied if isinstance(valfmt, str): valfmt = matplotlib.ticker.StrMethodFormatter(valfmt) # Loop over the data and create a `Text` for each "pixel". # Change the text's color depending on the data. texts = [] for i in range(data.shape[0]): for j in range(data.shape[1]): kw.update(color=textcolors[im.norm(data[i, j]) > threshold]) text = im.axes.text(j, i, valfmt(data[i, j], None), **kw) texts.append(text) return texts The above now allows us to keep the actual plot creation pretty compact. .. code-block:: python fig, ax = plt.subplots() im, cbar = heatmap(harvest, vegetables, farmers, ax=ax, cmap="YlGn", cbarlabel="harvest [t/year]") texts = annotate_heatmap(im, valfmt="{x:.1f} t") fig.tight_layout() plt.show() .. image:: /gallery/images_contours_and_fields/images/sphx_glr_image_annotated_heatmap_002.png :class: sphx-glr-single-img Some more complex heatmap examples ---------------------------------- In the following we show the versitality of the previously created functions by applying it in different cases and using different arguments. .. code-block:: python np.random.seed(19680801) fig, ((ax, ax2), (ax3, ax4)) = plt.subplots(2, 2, figsize=(8, 6)) # Replicate the above example with a different font size and colormap. im, _ = heatmap(harvest, vegetables, farmers, ax=ax, cmap="Wistia", cbarlabel="harvest [t/year]") annotate_heatmap(im, valfmt="{x:.1f}", size=7) # Create some new data, give further arguments to imshow (vmin), # use an integer format on the annotations and provide some colors. data = np.random.randint(2, 100, size=(7, 7)) y = ["Book {}".format(i) for i in range(1, 8)] x = ["Store {}".format(i) for i in list("ABCDEFG")] im, _ = heatmap(data, y, x, ax=ax2, vmin=0, cmap="magma_r", cbarlabel="weekly sold copies") annotate_heatmap(im, valfmt="{x:d}", size=7, threshold=20, textcolors=["red", "white"]) # Sometimes even the data itself is categorical. Here we use a # :class:`matplotlib.colors.BoundaryNorm` to get the data into classes # and use this to colorize the plot, but also to obtain the class # labels from an array of classes. data = np.random.randn(6, 6) y = ["Prod. {}".format(i) for i in range(10, 70, 10)] x = ["Cycle {}".format(i) for i in range(1, 7)] qrates = np.array(list("ABCDEFG")) norm = matplotlib.colors.BoundaryNorm(np.linspace(-3.5, 3.5, 8), 7) fmt = matplotlib.ticker.FuncFormatter(lambda x, pos: qrates[::-1][norm(x)]) im, _ = heatmap(data, y, x, ax=ax3, cmap=plt.get_cmap("PiYG", 7), norm=norm, cbar_kw=dict(ticks=np.arange(-3, 4), format=fmt), cbarlabel="Quality Rating") annotate_heatmap(im, valfmt=fmt, size=9, fontweight="bold", threshold=-1, textcolors=["red", "black"]) # We can nicely plot a correlation matrix. Since this is bound by -1 and 1, # we use those as vmin and vmax. We may also remove leading zeros and hide # the diagonal elements (which are all 1) by using a # :class:`matplotlib.ticker.FuncFormatter`. corr_matrix = np.corrcoef(np.random.rand(6, 5)) im, _ = heatmap(corr_matrix, vegetables, vegetables, ax=ax4, cmap="PuOr", vmin=-1, vmax=1, cbarlabel="correlation coeff.") def func(x, pos): return "{:.2f}".format(x).replace("0.", ".").replace("1.00", "") annotate_heatmap(im, valfmt=matplotlib.ticker.FuncFormatter(func), size=7) plt.tight_layout() plt.show() .. image:: /gallery/images_contours_and_fields/images/sphx_glr_image_annotated_heatmap_003.png :class: sphx-glr-single-img ------------ References """""""""" The usage of the following functions and methods is shown in this example: .. code-block:: python matplotlib.axes.Axes.imshow matplotlib.pyplot.imshow matplotlib.figure.Figure.colorbar matplotlib.pyplot.colorbar .. _sphx_glr_download_gallery_images_contours_and_fields_image_annotated_heatmap.py: .. only :: html .. container:: sphx-glr-footer :class: sphx-glr-footer-example .. container:: sphx-glr-download :download:`Download Python source code: image_annotated_heatmap.py ` .. container:: sphx-glr-download :download:`Download Jupyter notebook: image_annotated_heatmap.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature Keywords: matplotlib code example, codex, python plot, pyplot `Gallery generated by Sphinx-Gallery `_