From f7cb9cde135dce4245238ecac6566947a6e251d8 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Fri, 16 Jun 2023 22:17:30 +0200 Subject: [PATCH] Improve docs about customising tables from the config --- docs/core/reports/customisation.md | 41 +++++++++++++++++++++--------- multiqc/plots/table.py | 2 +- 2 files changed, 30 insertions(+), 13 deletions(-) diff --git a/docs/core/reports/customisation.md b/docs/core/reports/customisation.md index f3e07fd02f..678f8947d3 100644 --- a/docs/core/reports/customisation.md +++ b/docs/core/reports/customisation.md @@ -528,20 +528,29 @@ custom_plot_config: Much like with the custom plot config above, you can override almost any configuration options for tables. To see what's available, read the documentation about [Creating a table](#creating-a-table) below. -Tables have configuration at two levels. Table-wide configs are the same as plot configs and can -be overridden with `custom_plot_config` as described above. +Tables have configuration at two levels: -Headers have their own configuration which can be overriden with `custom_table_header_config`. +1. Entire table -Examples are often more useful for this kind of thing than words, so here are a few: +- Affects all columns and data. These configs are the same as _plot configs_ and can be overridden with `custom_plot_config` as described in the [Customising plots](#customising-plots) section above. -For the Picard HSMetrics table, we can use a custom table header for the first column -and change the default minimum value for the colour scale for all columns: +2. Specific columns -> Here `min` is a _header_ config but we're setting it at table config level. -> This means it will be used as a default for all columns in the table if the module -> doesn't itself define anything specific for that column. -> If it does, you need to overwrite that specific column using `custom_table_header_config` +- Table columns (headers) have their own configuration scope:`custom_table_header_config`. See below. + +Here are a couple of examples: + +### Entire table + +Here we are customising the _Picard HSMetrics_ table. +We're setting a non-standard title for the first column (usually _"Sample name"_) and changing the default minimum value for the colour scale for _all_ columns. + +:::note +Here `min` is a _header_ config but we're setting it at _table config_ level. +This means it will be used as a default for all columns in the table if the module +doesn't itself define anything specific for that column. +If it does, you need to overwrite that specific column using `custom_table_header_config`. +::: ```yaml custom_plot_config: @@ -550,8 +559,9 @@ custom_plot_config: min: 1000 ``` -Now for header-specific changes. -To change the number of decimals used in the General Statistics table for the Qualimap _Mean Coverage_ column: +### Specific column + +To change the number of decimals used in the General Statistics table for the single column Qualimap _Mean Coverage_: ```yaml custom_table_header_config: @@ -560,6 +570,13 @@ custom_table_header_config: format: "{:,.20f}" ``` +The first key is the table ID, the second is the header ID for the column you want to change. + +:::tip +The easiest way to find these IDs is by clicking _Configure Columns_ above the table you want to customise. +The table ID is shown at the top of the modal window. The _ID_ column shows the column (header) ID. +::: + ### Hiding columns Report tables such as the General Statistics table can get quite wide. To help with this, diff --git a/multiqc/plots/table.py b/multiqc/plots/table.py index 7d377e7a2d..56fd85594a 100644 --- a/multiqc/plots/table.py +++ b/multiqc/plots/table.py @@ -397,7 +397,7 @@ def make_table(dt):

{title}: Columns

-

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

+

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: {tid}