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plot_altair_ccc_tissue.py
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plot_altair_ccc_tissue.py
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#sys.path.append("/path/to/parent/directory/of/altairThemes.py")
import pandas as pd
import matplotlib
import altair as alt
import altairThemes # assuming you have altairThemes.py at your current directoy or your system knows the path of this altairThemes.py.
# register the custom theme under a chosen name
#alt.themes.register("publishTheme", altairThemes.publishTheme)
# enable the newly registered theme
#alt.themes.enable("publishTheme")
filepath = '/cluster/home/t116508uhn/64630/ccc_th95_tissue_plot_woBlankEdges.csv' #'/mnt/data0/fatema/public/ccc_plot/ccc_th95_tissue_plot.csv'
savepath = '/cluster/home/t116508uhn/64630/' #'/mnt/data0/fatema/public/ccc_plot/'
data_list_pd = pd.read_csv(filepath)
set1 = altairThemes.get_colour_scheme("Set1", len(data_list_pd["component_label"].unique()))
chart = alt.Chart(data_list_pd).mark_point(filled=True, opacity = 1).encode(
alt.X('X', scale=alt.Scale(zero=False), axis=alt.Axis(grid=False)),
alt.Y('Y', scale=alt.Scale(zero=False), axis=alt.Axis(grid=False)),
shape = "pathology_label",
color=alt.Color('component_label:N', scale=alt.Scale(range=set1)),
tooltip=['component_label']
)#.configure_legend(labelFontSize=6, symbolLimit=50)
chart.save(save_path+'ccc_th95_tissue_plot_woBlankEdges.html')