Example of oncoplot¶

In [1]:

from pyMut.input import read_maf


maf_path = "../../../src/pyMut/data/examples/MAF/tcga_laml.maf.gz"
print(f'📂 Loading file: {maf_path}')

# Read the MAF file and create the PyMutation object
py_mutation = read_maf(maf_path,assembly="37")

from pyMut.input import read_maf maf_path = "../../../src/pyMut/data/examples/MAF/tcga_laml.maf.gz" print(f'📂 Loading file: {maf_path}') # Read the MAF file and create the PyMutation object py_mutation = read_maf(maf_path,assembly="37")

2025-08-01 00:58:01,467 | INFO | pyMut.input | Starting MAF reading: ../../../src/pyMut/data/examples/MAF/tcga_laml.maf.gz
2025-08-01 00:58:01,468 | INFO | pyMut.input | Loading from cache: ../../../src/pyMut/data/examples/MAF/.pymut_cache/tcga_laml.maf_8bfbda65c4b23428.parquet
2025-08-01 00:58:01,494 | INFO | pyMut.input | Cache loaded successfully in 0.03 seconds

📂 Cargando archivo: ../../../src/pyMut/data/examples/MAF/tcga_laml.maf.gz

In [2]:

py_mutation.configure_high_quality_plots()

py_mutation.configure_high_quality_plots()

In [3]:

py_mutation.oncoplot()

py_mutation.oncoplot()

Processing 193 samples and data from 2091 variants...
Processed matrix: 1611 genes x 193 samples
Genes with mutations: 1611
Applying standard cascade algorithm (maftools)...
Cascade applied:
  - Genes sorted by frequency: 10
  - Samples sorted by cascade algorithm: 180
  - Final samples shown: 180

/home/luisruimore/Escritorio/TFG/src/pyMut/visualizations/oncoplot.py:416: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`
  numeric_matrix = plot_matrix.replace(value_to_num)
/home/luisruimore/Escritorio/TFG/src/pyMut/visualizations/oncoplot.py:490: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.
  numeric_matrix = plot_matrix.applymap(lambda x: value_to_num[x])

Oncoplot created successfully:
  - 10 genes
  - 180 samples
  - 9 variant types
  - Standard cascade algorithm applied (maftools)

Out[3]: