automatic and custom vertical lines in scatter plots

[carlocolantuoni]

it looks like the nemo devel now automatically adds a vertical line at 0 in each scatterplot. i like it most of the time, but sometimes its not ideal - could we make it optional? could we also add custom vertical lines at user-defined values along with user defined labels? could we also specify solid or dotted/dashed?

[adkinsrs]

@carlocolantuoni are you referring to the plot with jitter in it that has the vertical line at 0? If so, that's completely unintentional... I'm actually hiding a box plot in the background and some of the boxplot still wants to show up. I'm having a heck of a time trying to get this to play nice.

[carlocolantuoni]

all my scatter plots now have a solid vertical line at 0 on the x axis

[adkinsrs]

I see now. In plotly there is a true/false setting for the zeroline, which is True by default. If were to add user-defined lines, this would require me to disable that and add additional annotations to the plot. I feel this is a good candidate to add to a set of "advanced" settings.

[hertzron]

hi, it would be great if when we discuss this type of issues whoever posts a comment or feedback also puts a small screen capture. this will save others who are trying to follow along a lot of time in trying to replicate these scenarios and possibly provide good feedback.

R.

On Tue, Aug 11, 2020 at 2:40 PM Shaun Adkins notifications@github.com wrote:

I see now. In plotly there is a true/false setting for the zeroline, which is True by default. If were to add user-defined lines, this would require me to disable that and add additional annotations to the plot. I feel this is a good candidate to add to a set of "advanced" settings.

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[adkinsrs]

@hertzron this is what Carlo is referring to. Currently for axes for numerical groups, there is a line at 0. He wants the option in the UI to annotate the x- or y-intercept where these lines should go and style the line to be solid/dashed/etc.

[hertzron]

thanks!

On Tue, Aug 11, 2020 at 3:08 PM Shaun Adkins notifications@github.com wrote:

[image: newplot] https://user-images.githubusercontent.com/5665914/89938277-43846d00-dbe4-11ea-84d8-74f9ac1beb94.png

@hertzron https://github.com/hertzron this is what Carlo is referring to. Currently for axes for numerical groups, there is a line at 0. He wants the option in the UI to annotate the x- or y-intercept where these lines should go and style the line to be solid/dashed/etc.

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[adkinsrs]

Added option for vertical lines. I do not have any error checking in place for if the x-axis is categorical

[carlocolantuoni]

these are looking great in the curator (see below) but dont appear in the view of the profile.

[carlocolantuoni]

another note here : just like the vertical lines, the Y-axis labels appear when in the curator, but not in the profile view.

[carlocolantuoni]

[adkinsrs]

@carlocolantuoni I may have failed to save the vertical line properties in the mysql database or failed to retrieve the property out of the mysql database for that particular view... I'll look into it. As for the y-axis title, I have a hunch it is there but is beyond the container boundary. This issue was resolved via a code commit but I believe it that code has not been pushed to the NeMO server yet.

[carlocolantuoni]

cool, thnx

[adkinsrs]

@carlocolantuoni I checked the v-line issue and apparently I had fixed it but the code is not deployed on the nemoanalytics server yet. I was able to view the v-lines in the profile view on devel.umgear.org.

[carlocolantuoni]

thats good. were there y axis labels?

[adkinsrs]

[carlocolantuoni]

great - so it looks like both lines and labels will be good when u move the changes in devel to the main page - is that right? carlo

On Mon, Nov 16, 2020 at 11:56 AM Shaun Adkins notifications@github.com wrote:

[image: Screen Shot 2020-11-16 at 11 54 47 AM] https://user-images.githubusercontent.com/5665914/99283209-af3d2e00-2802-11eb-980a-64b79ee7b887.png

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-- Carlo

[adkinsrs]

Correct. I have formally issued a pull request so @jorvis can add my changes to the main code branch, which can then be deployed out.

[carlocolantuoni]

great!

On Mon, Nov 16, 2020 at 3:26 PM Shaun Adkins notifications@github.com wrote:

Correct. I have formally issued a pull request so @jorvis https://github.com/jorvis can add my changes to the main code branch, which can then be deployed out.

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-- Carlo

[adkinsrs]

@jorvis is pushing this fix to gEAR and nemoanalytics before the end of the day.

[carlocolantuoni]

great! thnx

On Tue, Nov 17, 2020 at 12:00 PM Shaun Adkins notifications@github.com wrote:

@jorvis https://github.com/jorvis is pushing this fix to gEAR and nemoanalytics before the end of the day.

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-- Carlo

[carlocolantuoni]

it looks great, except the Y-axis labels are not being dynamically generated. it looks like the static label from the curation (where the curator page asks for an example gene to use in designing the view) is being carried forward. for example, when i searched for the "FEZF2" gene, the plots come up with labels that include the gene name used in the curation, but - the data is from the FEZF2 gene (see screen cap below). this mis labeling of the gene on Yaxis happens for every plot in the profile. [image: image.png]

On Tue, Nov 17, 2020 at 1:23 PM Carlo Colantuoni colantuonicarlo@gmail.com wrote:

great! thnx

On Tue, Nov 17, 2020 at 12:00 PM Shaun Adkins notifications@github.com wrote:

@jorvis https://github.com/jorvis is pushing this fix to gEAR and nemoanalytics before the end of the day.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nemoarchive/analytics/issues/132#issuecomment-729063710, or unsubscribe https://github.com/notifications/unsubscribe-auth/AH7KC7VQFVPHUDSXP43FE5LSQKT3RANCNFSM4PYJAAUA .

-- Carlo

-- Carlo

[adkinsrs]

Can you re-upload your image? It is not showing in the comment.

[adkinsrs]

Also I believe the reason why the dynamic labeling is not happening is because of this codeblock in api/resources/plotly_data.py that happens immediately before data is returned:

        # Modify y-title so that gene display results plot is not misleading
        if y_title == "expression of {}".format(gene_symbol):
            y_title = None

Generally I unset the y_title variable, so I can set it dynamically only if the y-axis is the expression value and y-title is empty. I can change this code block to something like if gene_symbol in y_title: instead, so it handles more cases.

[carlocolantuoni]

the problem disappears if i re-save each curated view, so i guess there was an issue of the new code reading the previously saved views.

On Tue, Nov 17, 2020 at 2:41 PM Shaun Adkins notifications@github.com wrote:

Reopened #132 https://github.com/nemoarchive/analytics/issues/132.

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-- Carlo

[adkinsrs]

I'll keep the ticket open for now in case something happens again in a different context.