| 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') | |