Merge pull request #696 from bigbio/dev

Add QPX support and enhance PMultiQC documentation

Author: ypriverol

.github/workflows/python-app.yml

@@ -351,4 +351,27 @@ jobs:
         name: Upload results
         with:
           name: results_single_cell_diann
-          path: ./results_single_cell_diann
+          path: ./results_single_cell_diann
+
+  test_qpx:
+    needs: setup
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install package
+        run: pip install .
+      - name: Test qpx dataset
+        run: |
+          wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/qpx_example.zip
+          unzip -d ./qpx_example qpx_example.zip
+          multiqc --qpx-plugin ./qpx_example --config ./qpx_example/results/multiqc_config.yml -o ./results_qpx
+      - uses: actions/upload-artifact@v4
+        if: always()
+        name: Upload results
+        with:
+          name: results_qpx
+          path: ./results_qpx

README.md

@@ -71,6 +71,12 @@ pmultiqc supports the following data sources:
 7. **[nf-core/mhcquant](https://nf-co.re/mhcquant)** result files:
    - `mhcquant/results-*`: folder containing mhcquant results
 
+8. **[QPX](https://github.com/bigbio/qpx)** files:
+   - `*.psm.parquet`: QPX PSMs
+   - `*.pg.parquet`: QPX PG
+   - `*.feature.parquet`: QPX feature
+   - `*sdrf.tsv`: SDRF-Proteomics (optional)
+
 ## Installation
 
 ### Install from PyPI
@@ -163,6 +169,12 @@ multiqc --fragpipe-plugin /path/to/fragpipe/files -o ./report
 multiqc --mhcquant-plugin /path/to/mhcquant/files -o ./report
 ```
 
+#### For qpx files
+
+```bash
+multiqc --qpx-plugin /path/to/qpx/files -o ./report
+```
+
 ### Command-line Options
 
 | Option | Description | Default |
@@ -184,6 +196,7 @@ multiqc --mhcquant-plugin /path/to/mhcquant/files -o ./report
 | `--mzid-plugin` | Generate reports based on mzIdentML files | `False` |
 | `--fragpipe-plugin` | Generate reports based on FragPipe files | `False` |
 | `--mhcquant-plugin` | Generate reports based on mhcquant files | `False` |
+| `--qpx-plugin` | Generate reports based on qpx files | `False` |
 | `--disable-hoverinfo` | Disable interactive hover tooltips in the plots | `False` |
 
 ## QC Metrics and Visualizations

docs/README.md

@@ -91,6 +91,12 @@ pmultiqc supports the following data sources:
 ### 7. [nf-core/mhcquant](https://nf-co.re/mhcquant) result files:
    - `mhcquant/results-*`: folder containing mhcquant results
 
+8. **[QPX](https://github.com/bigbio/qpx)** files:
+   - `*.psm.parquet`: QPX PSMs
+   - `*.pg.parquet`: QPX PG
+   - `*.feature.parquet`: QPX feature
+   - `*sdrf.tsv`: SDRF-Proteomics (optional)
+
 ## 💾 Installation
 
 ### Install from PyPI
@@ -178,6 +184,12 @@ multiqc --fragpipe-plugin /path/to/fragpipe/files -o ./report
 multiqc --mhcquant-plugin /path/to/mhcquant/files -o ./report
 ```
 
+#### For qpx files
+
+```bash
+multiqc --qpx-plugin /path/to/qpx/files -o ./report
+```
+
 ### Command-line Options
 
 | Option | Description | Default |
@@ -199,6 +211,7 @@ multiqc --mhcquant-plugin /path/to/mhcquant/files -o ./report
 | `--mzid-plugin` | Generate reports based on mzIdentML files | `False` |
 | `--fragpipe-plugin` | Generate reports based on FragPipe files | `False` |
 | `--mhcquant-plugin` | Generate reports based on mhcquant files | `False` |
+| `--qpx-plugin` | Generate reports based on qpx files | `False` |
 | `--disable-hoverinfo` | Disable interactive hover tooltips in the plots | `False` |
 
 ## 📊 QC Metrics and Visualizations
@@ -255,6 +268,7 @@ You can find example reports on the [docs page](https://bigbio.github.io/pmultiq
 | mzIdentML with MGF | mzIdentML with MGF files | [mzIdentML with MGF Example](https://pmultiqc.quantms.org/PXD054720/multiqc_report.html) ([disable_hoverinfo](https://pmultiqc.quantms.org/PXD054720_disable_hoverinfo/multiqc_report.html)) | [PXD054720 folder](https://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD054720/) |
 | FragPipe | FragPipe results | [FragPipe Example](https://pmultiqc.quantms.org/PXD062399/multiqc_report.html) ([disable_hoverinfo](https://pmultiqc.quantms.org/PXD062399_disable_hoverinfo/multiqc_report.html)) | [PXD062399.zip](https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/PXD062399.zip) |
 | mhcquant | mhcquant results | [mhcquant Example](https://pmultiqc.quantms.org/mhcquant/multiqc_report.html) ([disable_hoverinfo](https://pmultiqc.quantms.org/mhcquant_disable_hoverinfo/multiqc_report.html)) | [mhcquant_3-1-0_results.zip](https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/mhcquant/mhcquant_3-1-0_results.zip) |
+| QPX | QPX results | [QPX Example](https://pmultiqc.quantms.org/qpx/multiqc_report.html) ([disable_hoverinfo](https://pmultiqc.quantms.org/qpx_disable_hoverinfo/multiqc_report.html)) | [qpx_example.zip](https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/qpx_example.zip) |
 
 ### 🔍 Large-Scale Dataset Reports
 

docs/config.json

@@ -227,6 +227,22 @@
             ],
             "path": "docs/mhcquant_disable_hoverinfo",
             "file_type": ["mhcquant", "disable_hoverinfo"]
+        },
+        {
+            "accession": "qpx",
+            "urls": [
+                "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/qpx_example.zip"
+            ],
+            "path": "docs/qpx",
+            "file_type": ["qpx", ""]
+        },
+        {
+            "accession": "qpx_disable_hoverinfo",
+            "urls": [
+                "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/qpx_example.zip"
+            ],
+            "path": "docs/qpx_disable_hoverinfo",
+            "file_type": ["qpx", "disable_hoverinfo"]
         }
     ]
 }

docs/update_examples.py

@@ -179,6 +179,16 @@ def run_pmultiqc(download_path, report_path, plugin_type):
         ]
     elif plugin_name == "diann":
         command = ["multiqc", "--diann-plugin", download_path, "-o", report_path]
+    elif plugin_name == "qpx":
+        command = [
+            "multiqc",
+            "--qpx-plugin",
+            download_path,
+            "--config",
+            os.path.join(download_path, "results/multiqc_config.yml"),
+            "-o",
+            report_path
+        ]
     else:
         raise ValueError(f"Unknown plugin type: {plugin_name}")
 

pmultiqc/cli.py

@@ -82,5 +82,6 @@ def print_version(ctx, params, value):
 mhcquant_plugin = click.option(
     "--mhcquant-plugin", "mhcquant_plugin", is_flag=True, help="Enable mhcquant plugin"
 )
+qpx_plugin = click.option("--qpx-plugin", "qpx_plugin", is_flag=True, help="Enable qpx plugin")
 disable_hoverinfo = click.option(
     "--disable-hoverinfo", "disable_hoverinfo", is_flag=True, help="Disable hoverinfo")

pmultiqc/main.py

@@ -179,4 +179,31 @@ def pmultiqc_plugin_execution_start():
             {"pmultiqc/fragger_params": {"fn": "*.params", "num_lines": 0}},
         )
 
+    # QPX file (https://github.com/bigbio/qpx)
+    if "pmultiqc/qpx_psm" not in  config.sp:
+        config.update_dict(
+            config.sp,
+            {"pmultiqc/qpx_psm": {"fn": "*.psm.parquet", "num_lines": 0}},
+        )
+    if "pmultiqc/qpx_pg" not in  config.sp:
+        config.update_dict(
+            config.sp,
+            {"pmultiqc/qpx_pg": {"fn": "*.pg.parquet", "num_lines": 0}},
+        )
+    if "pmultiqc/qpx_feature" not in  config.sp:
+        config.update_dict(
+            config.sp,
+            {"pmultiqc/qpx_feature": {"fn": "*.feature.parquet", "num_lines": 0}},
+        )
+    if "pmultiqc/qpx_run" not in  config.sp:
+        config.update_dict(
+            config.sp,
+            {"pmultiqc/qpx_run": {"fn": "*.run.parquet", "num_lines": 0}},
+        )
+    if "pmultiqc/qpx_sample" not in config.sp:
+        config.update_dict(
+            config.sp,
+            {"pmultiqc/qpx_sample": {"fn": "*.sample.parquet", "num_lines": 0}},
+        )
+
     config.update({"log_filesize_limit": 200 * pow(1024, 3), "thousandsSep_format": ""})

pmultiqc/modules/common/common_utils.py

@@ -897,3 +897,28 @@ def mods_statistics(df: pd.DataFrame, run_col: str):
                     "cats": list(sorted(modified_cats, key=lambda x: (x == "Modified (Total)", x)))}
 
     return modified_dict
+
+
+# if missed.cleavages is not given, it is assumed that Trypsin was used for digestion
+def cal_miss_cleavages(sequence, enzyme):
+    if enzyme == "Trypsin/P":
+        miss_cleavages = len(sequence[:-1]) - len(
+            sequence[:-1].replace("K", "").replace("R", "").replace("P", "")
+        )
+    elif enzyme == "Arg-C":
+        miss_cleavages = len(sequence[:-1]) - len(sequence[:-1].replace("R", ""))
+    elif enzyme == "Asp-N":
+        miss_cleavages = len(sequence[:-1]) - len(
+            sequence[:-1].replace("B", "").replace("D", "")
+        )
+    elif enzyme == "Chymotrypsin":
+        miss_cleavages = len(sequence[:-1]) - len(
+            sequence[:-1].replace("F", "").replace("W", "").replace("Y", "").replace("L", "")
+        )
+    elif enzyme == "Lys-C":
+        miss_cleavages = len(sequence[:-1]) - len(sequence[:-1].replace("K", ""))
+    else:
+        miss_cleavages = len(sequence[:-1]) - len(
+            sequence[:-1].replace("K", "").replace("R", "")
+        )
+    return miss_cleavages

pmultiqc/modules/common/dia_utils.py

@@ -35,7 +35,7 @@ def parse_diann_report(
         heatmap_color_list,
         sample_df,
         ms_with_psm,
-        quantms_modified,
+        modified,
         ms_paths,
         file_df=None,
         msstats_input_valid=False
@@ -64,7 +64,7 @@ def parse_diann_report(
 
     # Process run-specific data (requires Modifications column from _process_modifications)
     if modifications_ok:
-        cal_num_table_data = _process_run_data(report_data, ms_with_psm, quantms_modified, file_df)
+        cal_num_table_data = _process_run_data(report_data, ms_with_psm, modified, file_df)
     else:
         log.warning("Skipping run data processing due to missing modifications data")
         cal_num_table_data = {"sdrf_samples": {}, "ms_runs": {}}
@@ -82,7 +82,7 @@ def parse_diann_report(
         peptide_search_score,
         ms_with_psm,
         cal_num_table_data,
-        quantms_modified,
+        modified,
         ms_without_psm,
         peptide_length
     )
@@ -591,6 +591,19 @@ def draw_protein_table(sub_sections, table_data, headers, report_type):
             * Peptides_Number: The number of peptides for each protein.
             * Average Intensity: Average intensity of each protein(0 or NA ignored).
             """
+    elif report_type == "qpx":
+        description_text = """
+            This plot shows the quantification information of proteins in the final result (quantms.io pg.parquet).
+            """
+        helptext_text = """
+            The quantification information of proteins is obtained from the `intensity` column of pg.parquet.
+            Proteins are sorted by average intensity, and the most abundant ones are shown.
+
+            * Peptides_Number: The number of distinct peptide sequences for each protein.
+            * Average Intensity: log10 of the average protein group intensity across runs (0 or NA ignored).
+            * Global Q-value: The best (lowest) global q-value reported for the protein group.
+            * Protein intensity in each condition: log10 average intensity within that condition.
+            """
     else:
         description_text = ""
         helptext_text = ""

pmultiqc/modules/common/plots/dia.py

@@ -4,6 +4,7 @@
 from multiqc.plots import heatmap, box, bargraph, linegraph
 
 from pmultiqc.modules.common.plots.general import (
+    summarise_box_data,
     plot_html_check,
     plot_data_check
 )
@@ -120,6 +121,10 @@ def draw_dia_intensity_dis(sub_section, df, sdrf_file_df):
         "save_data_file": False,
     }
 
+    # Summarise to box statistics so a large report stays interactive rather than
+    # falling back to a flat image that does not fill the panel.
+    box_data = summarise_box_data(box_data)
+
     box_html = box.plot(list_of_data_by_sample=box_data, pconfig=draw_config)
 
     # box_html.flat