Create Patchseq profile for Flagship paper (Fig4)

[brianherb]

Patchseq -

@jorvis - the attached IT_test.zip file contains two files - a svg (IT_test.svg) and a data matrix (ITexpression.csv). The goal is to color the rectangles at the bottom of the image like a heatmap reflecting the expression from the data matrix.

IT_test.zip

[jorvis]

Can you upload the actual datafile to the devel version of NeMO? Then I can test the SVG on there.

[brianherb]

@jorvis - just checking, this site: https://gear-devel.nemoanalytics.org/ ?

[brianherb]

@jorvis - take a look at dataset 'Flagship Patchseq IT Test' - 403cf3ea-c5cb-7add-3142-a96945152f63

[jorvis]

Like this? (currently on production)

[brianherb]

OOOOOOOOOH! So does that mean it worked as is? That is fabulous!

[jorvis]

Yep, all good. I only had to modify our SVG processor to look for 'rect' elements to color in addition to the usual path and circle elements.

[carlocolantuoni]

gorgeous guys

On Fri, Oct 9, 2020 at 4:10 PM Joshua Orvis notifications@github.com wrote:

Yep, all good.

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-- Carlo

[brianherb]

This is how I'm thinking of grouping neuron types - some have two rows, but each will be their own 'window'

Lamp5

Sncg / Vip

Sst

Pvalb

IT

ET

[carlocolantuoni]

wow - very cool - after u and joshua implement all this, maybe you could pick a time to show us all how this works live along with the other flagship profile element you've built (like the MERfish etc). great to see it coming together

On Tue, Oct 13, 2020 at 11:43 AM Brian Herb notifications@github.com wrote:

This is how I'm thinking of grouping neuron types - some have two rows, but each will be their own 'window'

Lamp5 [image: image] https://user-images.githubusercontent.com/13540148/95883381-dbb7e300-0d48-11eb-8826-5043e9f2ea57.png

Sncg / Vip [image: image] https://user-images.githubusercontent.com/13540148/95883029-66e4a900-0d48-11eb-8902-e5486b5aacae.png

Sst [image: image] https://user-images.githubusercontent.com/13540148/95883150-9693b100-0d48-11eb-87e4-4c50b8506ef6.png

Pvalb [image: image] https://user-images.githubusercontent.com/13540148/95883275-c04cd800-0d48-11eb-870b-9cceda5c1a9f.png

IT [image: image] https://user-images.githubusercontent.com/13540148/95883474-f8541b00-0d48-11eb-9837-9028c4b7b4a8.png

ET [image: image] https://user-images.githubusercontent.com/13540148/95883543-11f56280-0d49-11eb-8485-79f481d74bce.png

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-- Carlo

[brianherb]

New datasets on nemoanalytics:
(celltype - dataset name - unique id)

IT - Flagship Patchseq IT - 097fca87-8679-054b-d223-46ba4618f624

Lamp5 - Flagship Patchseq Lamp5 - 98db4be8-4a23-6a19-70ce-75444c79b6ed

Pvalb - Flagship Patchseq Pvalb - c0f77e66-ab22-6e4a-642a-c41f1ec6b9a3

ET - Flagship Patchseq ET - 5a8a7aae-248e-206b-d239-5b584afe8978

Sncg/Vip - Flagship Patchseq Sncg_Vip - 15b97730-aee5-d142-b6d3-ca1bd3c79197

Sst - Flagship Patchseq Sst - f973b4f0-ed0a-9ddb-c6c7-2fa5e0817796

[brianherb]

A new profile named 'MOp Patchseq' has been created here: https://www.nemoanalytics.org/p?l=1206f7ce

Unfortunately when all panels are together they do not render properly. If there is just one panel in the profile, it looks fine, but putting two or more causes problems.

[brianherb]

[jorvis]

Yes, mixing a lot of wide images with different aspect ratios is a problem.

[brianherb]

Fixed issue by reducing the size of the background image.