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AllonKleinLab / SPRING_dev

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Changing expression colors #24

Closed justinesjw closed 3 years ago

justinesjw commented 3 years ago

Hi SPRING_dev team!

Thanks for the awesome tools!

I may have missed this, can you please guide me to where can I change the expression colors?

Currently it's green in color. For better visualization, I want more tones to it maybe a viridis. image

Thanks! Justine

AllonMKlein commented 3 years ago

Hi Justine! We haven’t implemented that at the GUI level yet. If you wanted to edit the code, it should be straightforward. Copying in Caleb and Sam in case they can quickly give the answer.

On Dec 1, 2020, at 1:18 AM, justinesjw notifications@github.com wrote:



Hi SPRING_dev team!

Thanks for the awesome tools!

I may have missed this, can you please guide me to where can I change the expression colors?

Currently it's green in color. For better visualization, I want more tones to it maybe a viridis. [image]https://urldefense.proofpoint.com/v2/url?u=https-3A__user-2Dimages.githubusercontent.com_26448066_100704096-2Dda697500-2D33df-2D11eb-2D8ad1-2D6780d306d099.png&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=k8xAWGirsd-UdOwtVp-_wvT_xZ_77NGM4A6xjZIgrkc&m=Ac9e7nUjClvnTsQVNxaBaMYwNLBZAwebague1kSy1vw&s=Ath0iaQMkcWZbg0LeR2z-OVt4m8r995JP0BKZ9ovPfY&e=

Thanks! Justine

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calebweinreb commented 3 years ago

Hi Justine,

We currently don't have the ability to swap in new colorscales. You could edit the code to interpolate between black and some color other than green, but using a colorscale like viridis would be more complicated. I think the easiest way for you to proceed would be the following:

1) Download the SPRING coordinates using the Download menu 2) The coordinates file should have three columns, the second and third columns are the x and y coordinates of each cell (note that y is usually flipped so you will have to use -y). The first column contains the (base-0) index of each cell with respect to the original expression matrix that you uploaded. 3) If you load the coordinates into R, python, matlab or whatever software you use, it should be possible to recreate the gene expression plot using your original gene expression data. The only way that the SPRING plot differs from the uploaded data is that the gene expression values are total-counts normalized, so you may want to include this step prior to plotting. 4) If you would like to included edges in the plot, the edges can also be downloaded and plotted behind the points.

On Tue, Dec 1, 2020 at 8:35 AM AllonKleinLab notifications@github.com wrote:

Hi Justine! We haven’t implemented that at the GUI level yet. If you wanted to edit the code, it should be straightforward. Copying in Caleb and Sam in case they can quickly give the answer.

On Dec 1, 2020, at 1:18 AM, justinesjw notifications@github.com wrote:



Hi SPRING_dev team!

Thanks for the awesome tools!

I may have missed this, can you please guide me to where can I change the expression colors?

Currently it's green in color. For better visualization, I want more tones to it maybe a viridis. [image]< https://urldefense.proofpoint.com/v2/url?u=https-3A__user-2Dimages.githubusercontent.com_26448066_100704096-2Dda697500-2D33df-2D11eb-2D8ad1-2D6780d306d099.png&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=k8xAWGirsd-UdOwtVp-_wvT_xZ_77NGM4A6xjZIgrkc&m=Ac9e7nUjClvnTsQVNxaBaMYwNLBZAwebague1kSy1vw&s=Ath0iaQMkcWZbg0LeR2z-OVt4m8r995JP0BKZ9ovPfY&e=>

Thanks! Justine

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justinesjw commented 3 years ago

Noted with thanks!

Hope you guys are doing well :)