Is your feature request related to a problem? Please describe.
It has come up with a few different users now that they would like to be able to look at the colored phenotype maps outside of the notebooks. As discussed in pipeline meeting a few weeks ago, it'd be good to save all of the colored phenotype maps in both pixel and cell clustering notebooks (and if the user wants to use custom colors, that is something they can do outside of the notebooks or come to office hours for help. FYI if someone does come to you guys for help with using custom colors, here is some example code: https://github.com/angelolab/ark-analysis/issues/773).
Describe the solution you'd like
The colored phenotype maps are already generated at the end of the Pixie notebooks for visualizing a subset of FOVs (plot_utils.plot_pixel_cell_cluster_overlay). Add a function to generate this colored phenotype map for all FOVs and save these to a directory called "pixel_mats_colored" or something like that.
Describe alternatives you've considered
Open to other suggestions.
Is your feature request related to a problem? Please describe. It has come up with a few different users now that they would like to be able to look at the colored phenotype maps outside of the notebooks. As discussed in pipeline meeting a few weeks ago, it'd be good to save all of the colored phenotype maps in both pixel and cell clustering notebooks (and if the user wants to use custom colors, that is something they can do outside of the notebooks or come to office hours for help. FYI if someone does come to you guys for help with using custom colors, here is some example code: https://github.com/angelolab/ark-analysis/issues/773).
Describe the solution you'd like The colored phenotype maps are already generated at the end of the Pixie notebooks for visualizing a subset of FOVs (
plot_utils.plot_pixel_cell_cluster_overlay). Add a function to generate this colored phenotype map for all FOVs and save these to a directory called "pixel_mats_colored" or something like that.Describe alternatives you've considered Open to other suggestions.