Add annotation labels for 3D plots #41

t0mdavid-m · 2024-09-28T12:36:14Z

This PR adds annotation labels for 3D plots. It can be tested easily using the PeakMap example jupyter notebook with the following sample DataFrame:

annotation_data = pd.DataFrame(
    {
        'leftWidth' : [212],
        'rightWidth' : [237],
        'IM_leftWidth' : [266],
        'IM_rightWidth' : [272],
        'color' : ['blue'],
        'name' : ['test'],
    }
)

While I was at it I also enabled the colors for the 2D visualizations (optional). I noticed that the rectangular 2D annotation was shown behind the plot data and made sure that it is displayed in the foreground.

I also noticed that annotation color and label for 3D plots is set using the input DataFrame. I propose moving these annotations to the annotation_data DataFrame to simplify the user experience.

jcharkow

Looks good just some minor suggestions. @singjc is more familiar with this so I would wait for his input before merging. I have not tested this out so assuming it does not break the existing 2D annotations.

pyopenms_viz/_core.py

jcharkow · 2024-09-28T20:03:31Z

pyopenms_viz/_matplotlib/core.py

@@ -732,7 +757,6 @@ def _add_box_boundaries(self, annotation_data):
                loc=matplotlibLegendLoc,
                title=self.feature_config.legend.title,
                prop={"size": self.feature_config.legend.fontsize},
-                bbox_to_anchor=self.feature_config.legend.bbox_to_anchor,


why is this line removed? I think this is needed for 2D legend placement

Sorry - I forgot to mention this. There seems to be a weird interaction between bbox_to_anchor and tight_layout(), where the plot gets resized when the legend is added. With the legend enabled not only the plot area shrinks (expected as the legend needs space) but also the entire figure gets resized in a strange way (unexpected).

If I disable tight_layout() in MATPLOTLIBPlot.show_default() or remove the bbox_to_anchor parameter the issues disappear.

How would you recommend to handle this issue?

If you disable tight_layout in MATPLOTLIBPlot.show_default() and keep bbox_to_anchor, after the plot get's generated, if you call plt.tight_layout(), does it still cause strange resizing?

No this did not resolve this issue on its own. Calling plt.tight_layout() after the fact seemed to not have any effect. Adjusting the anchoring of the bbox seems to result in nice plots (and should be more stable from what I can tell):

jcharkow · 2024-09-28T20:06:15Z

pyopenms_viz/_plotly/core.py

                    ),
+                    showlegend=True,


should legend showing be configurable?

I suppose we could make it optional for 3D plots as we have the in-plot annotation labels with this PR. For 2D-plots, the legend is currently the only way to pick a location so I am not sure how useful that would be.

We could add the same functionality but I am unsure how to best choose a good location for the in-plot annotation labels. Maybe we could allow for additional (x, y)-label-locations in annotation_data and let the user decide? What do you think?

Is this for adding in-plot text annotations 2D plots, that requires creating a dummy legend?

Any updates on this? I am not too familiar with Plotly so not sure what is best

Is this for adding in-plot text annotations 2D plots, that requires creating a dummy legend?

A dummy legend is not necessary for in-plot annotations afaik. I was just wondering how useful making the legend optional would be if there is no alternative. Thus, I suggested adding annotation labels to 2D-Plots as well but am unsure about a good general placement for the label.

I suppose we could require a set of coordinates for the user. This could be an optional feature for the 3D-Plots as well.

…z into annotation_labels

singjc

I tested and updated the manuscript_supp_config_gallery with the text annotations. It seems to work nicely with matplotlib and plotly. I did add a commit to allow adjusting the font size of the text annotations.

Other than Josh's comments/suggestions, I think everything looks good.

jcharkow · 2024-10-08T20:32:13Z

Hopefully we can merge soon?

…z into annotation_labels

singjc · 2024-10-11T18:15:12Z

Hopefully we can merge soon?

I think it is ready to merge.

t0mdavid-m · 2024-10-14T08:18:50Z

I agree @singjc .

Did you also see my reply to the comment regarding the configurable legend? @jcharkow @singjc

If we decide to implement it I suppose it could also be done in a separate PR.

singjc · 2024-10-14T17:23:27Z

I agree @singjc .

Did you also see my reply to the comment regarding the configurable legend? @jcharkow @singjc

If we decide to implement it I suppose it could also be done in a separate PR.

I think your suggestion for having additional x-y coordinate locations for positioning the labels could be an option? Then the legend could be set as configurable to display a legend or not. We could add it to this PR if it's not too much/won't take too long, or we could implement in another PR.

I think we would like to merge this PR relatively soon, since it is used in the manuscript.

t0mdavid-m · 2024-10-15T06:00:12Z

Agree that this PR should be merged asap. I will put this on my ToDo list and open a new PR when the changes are ready.

jcharkow · 2024-10-15T12:27:40Z

Will merge now

t0mdavid-m added 10 commits September 26, 2024 19:05

fix rectangle display

02965d0

support text annotations for mpl3d

9179cf7

move 3d computations to superclass

f237d01

unifiy colors in 2D and 3D

00c24ff

Merge branch 'main' into annotation_labels

e625445

fix 3D text display

158c7d0

fix rectangle display

c8cfec5

add dummy trace for legend

66b92b0

unify color handling

6993129

enable 3d annotations for plotly

400e417

jcharkow requested a review from singjc September 28, 2024 19:59

jcharkow approved these changes Sep 28, 2024

View reviewed changes

t0mdavid-m and others added 5 commits September 29, 2024 10:12

remove print statement

5b9c5e9

remove hardcoded annotation labels

eb83bf7

add: annotation fontsize

283dfd7

Merge branch 'annotation_labels' of github.com:t0mdavid-m/pyopenms_vi…

2d366a2

…z into annotation_labels

update: manuscript supp gallery

ef01127

singjc approved these changes Sep 30, 2024

View reviewed changes

t0mdavid-m added 2 commits October 9, 2024 17:14

fix legend placement

ae1e22e

Merge branch 'annotation_labels' of github.com:t0mdavid-m/pyopenms_vi…

4c5e3a9

…z into annotation_labels

jcharkow merged commit f91c651 into OpenMS:main Oct 15, 2024
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Add annotation labels for 3D plots #41

Add annotation labels for 3D plots #41

t0mdavid-m commented Sep 28, 2024

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t0mdavid-m Sep 29, 2024

singjc Sep 30, 2024

t0mdavid-m Oct 9, 2024

jcharkow Sep 28, 2024

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singjc Sep 30, 2024

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t0mdavid-m Oct 9, 2024

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t0mdavid-m commented Oct 14, 2024

singjc commented Oct 14, 2024

t0mdavid-m commented Oct 15, 2024

jcharkow commented Oct 15, 2024

Add annotation labels for 3D plots #41

Add annotation labels for 3D plots #41

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jcharkow commented Oct 8, 2024

singjc commented Oct 11, 2024

t0mdavid-m commented Oct 14, 2024

singjc commented Oct 14, 2024

t0mdavid-m commented Oct 15, 2024

jcharkow commented Oct 15, 2024