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f-hamidlab / nuclearpy

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Visualization of the clusters #4

Closed Marcel-Salier closed 2 years ago

Marcel-Salier commented 2 years ago

We need visualization of the clusters after the UMAP. And probably people would like to extract a subgroup of cells based on a marker or feature and restart everything over again.

fursham-h commented 2 years ago

This feature has already been implemented and added to the jupyter notebook (Cell #21). Fetch and pull the repository on Github Desktop to update to the latest version.

The code looks like this:

nga.plotDim(hue = "leiden", method="umap")

where hue allows you to colour cells based on any variables (including leiden or louvain clusters).

fursham-h commented 2 years ago

Reopening this issue. I think I understood what you want. You want to be able to choose cells from a scatter plot and visualize the distribution of features (intensities or other nuclear features) for the chosen cells

I will add a function chooseCells that allow lasso select data points from scatter plot and return a list of cells that can be used later.

fursham-h commented 2 years ago

Created chooseCells function that will plot a scatter plot with axes of choice, and allow selection of points (cells) using lassoselector. Works in Jupyter Notebook and Python console by opening a new window to display plot. Function can be further refined, but it is ready for use.

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