Plot.show() in Quarto notebook after if statement is not showing

Ask for help
1

I have a python cell in my Quarto notebook like:

#| echo: false

print(type(run_fastqc))
if run_fastqc:
    print(run_fastqc)
    fastqc_seqgc_plot = multiqc.get_plot("fastqc", "Per Sequence GC Content")
    fastqc_seqgc_plot.show()

However the plot is not showing up. The panel only shows:

<class 'bool'>
True

If I move the plot to outside the if statement

#| echo: false

print(type(run_fastqc))
if run_fastqc:
    print(run_fastqc)

fastqc_seqgc_plot = multiqc.get_plot("fastqc", "Per Sequence GC Content")
fastqc_seqgc_plot.show()

The plot shows up. Am I doing something silly (I have little understanding of python) or is this a bug?

Repo with reproducible example:GitHub - mahesh-panchal/nextflow-quarto-multiqc-demo: Using Quarto within Nextflow to make a MultiQC report

Open in Gitpod and use

pixi run nextflow

The last process makes the quarto notebook. The qmd is located in docs/multiqc_report. The html is written to results/report.

2

It seems using a ternary conditional is the solution here ( even with MultiQC 1.25 )

#| echo: false

# Have to use the ternary style syntax for if to make the plot show
# This doesn't work!
# if run_fastqc:
#     multiqc.get_plot("fastqc", "Sequence Counts").show()
# This does!
multiqc.get_plot("fastqc", "Sequence Counts").show() if run_fastqc else ""
1 Like
3

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.

4

Thanks again to bring this up and sorry for not getting back to your question sooner.
As we discussed in person, you are correct that display is needed to be called on show output unless it’s the last line in a cell. Jupyter automatically displays the output of the last line it called, but if it’s within a conditional, the output will be discarded.

Clarified that in the docs with Document use of display to show plots in notebooks by vladsavelyev · Pull Request #2938 · MultiQC/MultiQC · GitHub