Custom content works for interactive report but breaks for flat report

[barslmn]

Description of bug

I think problem is caused by giving the x as strings, but difference in the behavior seems like a bug. If this is an expected behavior I would need a way to indicate the x ticks to use the samplenames.

I have the following YAML file:

id: "xhet_section"
section_name: "X heterozygosity"
description: "This plot shows the fraction of heterozygous variants to total variants in X chromosome."
plot_type: "scatter"
pconfig:
  id: "Xhet_plot"
  title: "X heterozygosity plot"
  xlab: "samples"
  ylab: "Xhet"
data:
  150420-HG005-Homogeneity-01-Combined_S1: {x: 150420-HG005-Homogeneity-01-Combined_S1, y: 0.0126928}
  HG002-Run2_S1: {x: HG002-Run2_S1, y: 0.00921452}
  HG003Run03_S1: {x: HG003Run03_S1, y: 0.0128297}
  HG004run02_S1: {x: HG004run02_S1, y: 0.588197}
  NA24694-combined_S1: {x: NA24694-combined_S1, y: 0.00737769}
  NA24695-combined_S1: {x: NA24695-combined_S1, y: 0.532036}

The commands I am using:

  multiqc XhetRel --flat --force --fullnames --dirs --outdir XhetRel/ --filename multiqc_report_flat.html

  multiqc XhetRel --interactive --force --fullnames --dirs --outdir XhetRel/ --filename multiqc_report_interactive.html

Interactive one has the plot and completes without any errors:

/// MultiQC 🔍 | v1.21

| multiqc | Not cleaning sample names
| multiqc | Prepending directory to sample names
| multiqc | Search path : /content/XhetRel
| searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 67/67
| custom_content | xhet_section: Found 1 samples (scatter)
| bcftools | Found 13 stats reports
| relatedness2 | Found 1 valid relatedness2 matrices
| multiqc | Report : XhetRel/multiqc_report_interactive.html (overwritten)
| multiqc | Data : XhetRel/multiqc_report_interactive_data (overwritten)
| multiqc | MultiQC complete

Flat report gives an error and doesn't include the scatter plot. Output below.

File that triggers the error

Xhet_mqc.zip

MultiQC Error log

/// MultiQC 🔍 | v1.21

|           multiqc | Not cleaning sample names
|           multiqc | Prepending directory to sample names
|           multiqc | Search path : /content/XhetRel
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 67/67  
╭─────────────────────── Oops! The 'custom_content' MultiQC module broke... ───────────────────────╮
│ Please copy this log and report it at https://github.com/MultiQC/MultiQC/issues                  │
│ Please attach a file that triggers the error. The last file found was: XhetRel/Xhet_mqc.yaml     │
│                                                                                                  │
│ Traceback (most recent call last):                                                               │
│   File "/usr/local/lib/python3.10/dist-packages/multiqc/multiqc.py", line 751, in run            │
│     output = mod()                                                                               │
│   File "/usr/local/lib/python3.10/dist-packages/multiqc/modules/custom_content/custom_content.py │
│     parsed_modules[mod_id].add_cc_section(c_id, mod)                                             │
│   File "/usr/local/lib/python3.10/dist-packages/multiqc/modules/custom_content/custom_content.py │
│     plot = scatter.plot(mod["data"], pconfig)                                                    │
│   File "/usr/local/lib/python3.10/dist-packages/multiqc/plots/scatter.py", line 120, in plot     │
│     return scatter.plot(plotdata, pconfig)                                                       │
│   File "/usr/local/lib/python3.10/dist-packages/multiqc/plots/plotly/scatter.py", line 31, in pl │
│     return p.add_to_report(report)                                                               │
│   File "/usr/local/lib/python3.10/dist-packages/multiqc/plots/plotly/plot.py", line 248, in add_ │
│     html = self.flat_plot()                                                                      │
│   File "/usr/local/lib/python3.10/dist-packages/multiqc/plots/plotly/plot.py", line 298, in flat │
│     self._make_flat_fig(dataset),                                                                │
│   File "/usr/local/lib/python3.10/dist-packages/multiqc/plots/plotly/plot.py", line 426, in _mak │
│     return dataset.create_figure(layout, is_log, is_pct)                                         │
│   File "/usr/local/lib/python3.10/dist-packages/multiqc/plots/plotly/scatter.py", line 82, in cr │
│     x_std = np.std(x_values)                                                                     │
│   File "/usr/local/lib/python3.10/dist-packages/numpy/core/fromnumeric.py", line 3645, in std    │
│     return _methods._std(a, axis=axis, dtype=dtype, out=out, ddof=ddof,                          │
│   File "/usr/local/lib/python3.10/dist-packages/numpy/core/_methods.py", line 206, in _std       │
│     ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,                                    │
│   File "/usr/local/lib/python3.10/dist-packages/numpy/core/_methods.py", line 152, in _var       │
│     arrmean = umr_sum(arr, axis, dtype, keepdims=True, where=where)                              │
│ numpy.core._exceptions._UFuncNoLoopError: ufunc 'add' did not contain a loop with signature matc │
│                                                                                                  │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
|          bcftools | Found 13 stats reports
|      relatedness2 | Found 1 valid relatedness2 matrices
|           multiqc | Report      : XhetRel/multiqc_report_flat.html   (overwritten)
|           multiqc | Data        : XhetRel/multiqc_report_flat_data   (overwritten)
|           multiqc | MultiQC complete

Before submitting

• I have read the troubleshooting documentation.
• I am using the latest release of MultiQC.
• I have included a full MultiQC log, not truncated.
• I have attached an input file (.zip if necessary) that triggers the error.