Hatched and colored box on Matplotlib, empty on Illustrator

[françois_2115]

Hi everyone,

I am pretty new to Illustrator but my issue is not experience-related (at least it does not seem on a first approach).

I am using Matplotlib to plot some figures. Specifically, I perform a boxplot with seaborn and I use matplotlib features to color the box and hatch it. I then save it in svg. It looks like this (and it also looks like this in Inkscape):

Then I move to Illustrator and insert it using the File-> Place command. I obtain this:

As you can see, the hatching and the color of the previously hatched boxes has disappeared.

Any idea of where the problem comes from and how I can solve it?

Thanks!

[Monika Gause]

Exactly how is the hatching made? Can you share a demo file?

[françois_2115]

Thanks for your answer. Please find below the sequence of code I use to generate the plot in python. I use python 3.7.

        plt.subplots()
        ax = sns.boxplot(data=data_table_AI, x='data', y='quantitative data', order=['foo', 'bar', 'spam'],
                         hue='sub-data', hue_order=['eggs', 'parrot'], dodge=True)
        sns.swarmplot(data=data_table_AI, x='data', y='quantitative data', order=['foo', 'bar', 'spam'],
                      hue='sub-data', hue_order=['eggs', 'parrot'], dodge=True,
                      size=2.5, linewidth=1)
        # Set box colors based on tissue and box hatching for basal side
        hatch_pattern = '////'
        list_color = ['#FFCCCC', '#FFCCCC', '#CCCCCC', '#CCCCCC', '#CCCCFF', '#CCCCFF', None, None]
        i_box = 0
        for patch in ax.patches:
            if patch.__class__.__name__ != 'Rectangle':
                patch.set_facecolor(list_color[i_box])
                # The hue order is 'apical' then 'basal', so every second patch (i.e., odd-indexed) is basal
                if i_box % 2 == 1:
                    patch.set_hatch(hatch_pattern)  # Set hatching for basal boxes
                i_box += 1
        # Set points color and edge color
        for i, collection in enumerate(ax.collections):
            collection.set_edgecolor('k')
            collection.set_facecolor(list_color[i])
        # Capitalize the first letter of tissue labels
        tissue_labels = [label.get_text() for label in ax.get_xticklabels()]
        tissue_labels = [label.capitalize() for label in tissue_labels]
        ax.set_xticklabels(tissue_labels)
        # Set labels and title
        plt.xlabel('Data')
        plt.ylabel('Quantitative data')
        plt.legend().remove()
        plt.tight_layout()
        # Set statistical tests
        pairs = [(('foo', 'eggs'), ('foo', 'parrot')),
                 (('bar', 'eggs'), ('bar', 'parrot')),
                 (('spam', 'eggs'), ('spam', 'parrot'))]
        annotator = Annotator(ax, pairs, data=data_table_AI, x='data', y='quantitative data',
                              order=['foo', 'bar', 'spam'], hue='sub-data', hue_order=['eggs', 'parrot'])
        annotator.configure(test='Mann-Whitney', text_format='star', loc='outside')
        annotator.apply_and_annotate()
        plt.show()

[Monika Gause]

So that is code, but what does it create? A clipping mask?

[françois_2115]

I have no idea. In matplotlib it is called an artist, here is the definition based on matplotlib website (https://matplotlib.org/stable/tutorials/artists.html😞

"

There are three layers to the Matplotlib API.

• the matplotlib.backend_bases.FigureCanvas is the area onto which the figure is drawn

• the matplotlib.backend_bases.Renderer is the object which knows how to draw on the FigureCanvas

• and the matplotlib.artist.Artist is the object that knows how to use a renderer to paint onto the canvas.

"

I tried to look into the svg file code but there is nothing clearly tagged with 'hatch'. Do you have any hint on how I can retrieve some useful information for you to understand the source of the bug?

[Monika Gause]

Then probably you have produced something that Illustrator does not know. Maybe you can upload the SVG file?

Maybe you can open it in Inkscape and then export to PDF?

[françois_2115]

Here it is!

I can directly save it in pdf in matplotlib too; ideally, I would prefer to have it in svg but if I cannot, I will use pdf as you suggest.

[Monika Gause]

Any file will be interpreted by Illustrator as soon as you open it, since Illustrator's native format is AI. 

Your pattern is an actual pattern in the SVG and Illustrator cannot read it.

[françois_2115]

I understand - I would have loved to understand where the issue was coming from, just for the knowledge of it, beyond the practical aspect.

Thank you for the time you spent on this!