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0a476ff | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | import scanpy as sc
import pandas as pd
from matplotlib.pyplot import rc_context
from matplotlib.colors import LinearSegmentedColormap
from dataloader import load_singlecell_data,getEntrezGeneSymbol
from pathlib import Path
def umap_plot(input_data_key,input_data_value):
EntrezGeneSymbol = getEntrezGeneSymbol(input_data_key,input_data_value)
BASE_PATH = Path(__file__).parent
single_cell_data_path = str(BASE_PATH.parent / "Core data")
single_cell_data=load_singlecell_data(single_cell_data_path)
color_vars=['leiden',EntrezGeneSymbol]
# Define colour map as requested by the client (from grey to blue)
cmap = LinearSegmentedColormap.from_list("grey_to_blue", ["#d3d3d3", "blue"])
with rc_context({"figure.figsize": (6, 6)}):
sc.pl.umap(single_cell_data, color=color_vars, # plot UMAP
cmap=cmap,
# /* Reference 1 - taken from https://scanpy.readthedocs.io/en/stable/tutorials/plotting/core.html */
legend_loc="on data", # Place labels on the data
frameon=True,
legend_fontsize=4.5,
legend_fontoutline=1,)
# /* end of reference 1 */
return sc.pl
# umap_plot('EntrezGeneSymbol','THBS1') # EXAMPLE OF USAGE WITH GENESYMBOL
# umap_plot('EntrezGeneID','7057')
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