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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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Function to transform coloured spot from clustering to a coloured line #311

Open curiegat opened 2 years ago

curiegat commented 2 years ago

Dear Giotto Developers,

I am opening this issue to ask whether Giotto has/is currently develop a function to transform the coloured spot generated from the clustering on the spat-plot function.

I wonder this coloured line would be helpful to be integrated with the plot generated from spatDeconvPlot, as the coloured line will retain the information of brain region.

image

I generate this is the coloured line (picture above) manually. I draw the line based on the picture I obtained from this plot

image

And I used the first picture and combined it with plot from spatDeconvPlot

image

I think the coloured line is useful and would be very helpful for the package, and I wonder if you don't develop the function, would it be possible for us to add it?, because my friend and I are interested to create the function.

Looking forward for your response

Thank you for your time and best regards,

Agatha

drieslab commented 2 years ago

Hi Agatha,

Looks really nice. We're always happy to help and provide support for external developers / contributors. We are currently not working on a solution for this, but would be happy to think about potential interesting ways to implement and make it compatible with downstream visualizations.

Thanks for reaching out, Ruben

RubD commented 1 year ago

With the release of Giotto Suite 3.0 it should be straightforward to add this functionality. It would just depend on what we can expect in terms of input. Ideally, each line or polygon should be an x,y data frame.

name x y

line1 0 1 line1 2 3 line1 4 10 . . line99 85 96 line99 102 106

curiegat commented 1 year ago

Many thanks for notify me this information. My friend and I will try to create that function :)