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Option to hide rows by default in General Statistics table #541
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After sleeping on this idea, I think it's overly complicated. Instead, add configurable options to merge stats for modules that commonly have two outputs for PE data. eg. In the FastQC module code, merge General Statistics stats for |
I've came across a solution that could work for me and maybe for some others, although it's not working properly right now. let me know if you'd like me to open a proper issue with it of if you'd prefer to reopen this one. what I havestarting from fastq files and ending up with bam and vcf files, one ends up too with fastq associated reports and also with bam and vcf associated reports. the first ones are listed in General Statistics table with suffixes ( what I thoughtwhat happens if I hide all fastq related columns from the General Statistics table by default through the multiqc_config.yaml file? the data would be still there, but only the main sample lines with whole sample information would be visible, and the rest of columns would be accessible on demand through the Configure Columns button. what I found outif you hide all fastq related columns from the General Statistics table by default the fastq related empty rows keep being displayed by default, although single a touch on any checkbox in the Configure Columns section updates these columns to be displayed only if a fastq related column is selected, or to be hidden otherwise. what I requestI know that this behaviour is not the same thing as merging fastq data into main sample data as this issue started, which would be much more complicated indeed, but being able to hide already empty rows by default could be enough for most of us. also, being able to hide all columns from a section instead of having to write down all columns' ids in the configuration file would be a great plus. current exampletable_columns_visible:
fastp:
pct_duplication: False
after_filtering_q30_rate: False
after_filtering_q30_bases: False
after_filtering_gc_content: False
pct_surviving: False
pct_adapter: False
FastQC:
percent_duplicates: False
percent_gc: False
avg_sequence_length: False
percent_fails: False
total_sequences: False desired exampletable_columns_visible:
fastp: False
FastQC: False |
Hi @pancheto, It took me over a year, but I finally implemented your request! 🎉 This now works: table_columns_visible:
FastQC: False Updated docs: https://multiqc.info/docs/#hiding-columns Let me know if you find any problems, and thanks for the suggestion 👍 Phil |
A classic problem in MultiQC is rows in the General Statistics table that have sample name variants, resulting in partial rows that don't line up properly - eg.
sample_name
,sample_name_R1
,sample_name_R2
being split across three lines.I typically recommend that sample names have the
_R1
and_R2
suffixes removed, but then these results are completely absent from the report, including in the plots below.Instead, it could be nice to have a new option to hide rows in tables by default. These could be shown with a button above the table. It would need an option to limit this to a specific table ID (eg. only General Stats). Also have string and regex matches (we only have to match here).
This gets us to the better state of having all samples in the report, and
_R2
hidden in General Stats by default. We still need to truncate_R1
from sample names to get those ones to line up with the main sample basename, but I think this is still an improvement. This may be good enough to add to the MultiQC default config too...The text was updated successfully, but these errors were encountered: