Update plot_cpdb_heatmap.py (#67)

* Update plot_cpdb_heatmap.py * Update tests.yaml * Update tests.yaml * Update tests.yaml * Update tests.yaml * Update tests.yaml
zktuong · Apr 19, 2024 · 8da5379 · 8da5379
1 parent 642bb98
commit 8da5379
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Showing 2 changed files with 7 additions and 6 deletions.
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
@@ -84,15 +84,13 @@ jobs:
           coverage report
 
       - name: Upload coverage to Codecov
-        if: matrix.config.os == 'ubuntu-latest' && matrix.config.python-version == '3.10' && github.actor != 'dependabot[bot]'
-        uses: codecov/codecov-action@v1
+        if: matrix.config.os == 'ubuntu-latest' && matrix.config.python-version == '3.10' && github.actor != 'dependabot[bot]' &&  github.actor == 'zktuong'
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage.xml
-          directory: ./coverage/reports/
           env_vars: ${{ format('OS={0},PYTHON={1}', matrix.config.os, matrix.config.python-version) }}
           flags: unittests
           name: codecov-umbrella
-          fail_ci_if_error: true
-          path_to_write_report: ./coverage/codecov_report.txt
+          fail_ci_if_error: false
           verbose: true
diff --git a/ktplotspy/plot/plot_cpdb_heatmap.py b/ktplotspy/plot/plot_cpdb_heatmap.py
@@ -27,6 +27,7 @@ def plot_cpdb_heatmap(
     title: str = "",
     return_tables: bool = False,
     symmetrical: bool = True,
+    default_sep: str = DEFAULT_CPDB_SEP,
     **kwargs
 ) -> Union[sns.matrix.ClusterGrid, Dict]:
     """Plot cellphonedb results as total counts of interactions.
@@ -66,6 +67,8 @@ def plot_cpdb_heatmap(
         Whether to return the dataframes storing the interaction network.
     symmetrical : bool, optional
         Whether to return the sum of interactions as symmetrical heatmap.
+    default_sep : str, optional
+        The default separator used when CellPhoneDB was run.
     **kwargs
         Passed to seaborn.clustermap.
 
@@ -83,7 +86,7 @@ def plot_cpdb_heatmap(
     all_int = all_intr.iloc[:, col_start : all_intr.shape[1]].T
     all_int.columns = intr_pairs
     if cell_types is None:
-        cell_types = sorted(list(set([y for z in [x.split(DEFAULT_CPDB_SEP) for x in all_intr.columns[col_start:]] for y in z])))
+        cell_types = sorted(list(set([y for z in [x.split(default_sep) for x in all_intr.columns[col_start:]] for y in z])))
     cell_types_comb = ["|".join(list(x)) for x in list(product(cell_types, cell_types))]
     cell_types_keep = [ct for ct in all_int.index if ct in cell_types_comb]
     empty_celltypes = list(set(cell_types_comb) ^ set(cell_types_keep))