kegg-value-colors-txt

A TXT-type anvi’o artifact. This artifact is typically provided by the user for anvi’o to import into its databases, process, and/or use.

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Provided by

There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.

Required by

There are no anvi’o tools that require this artifact directly, which means it is most likely an end-product for the user.

Can be used by

anvi-draw-kegg-pathways

Description

This artifact is a TAB-delimited text file that gives a color of your choosing to each categorical value of a kegg-reaction-txt or kegg-compound-txt file drawn by anvi-draw-kegg-pathways.

A value column holds categorical values when the run gives --reaction-value-type categorical or --compound-value-type categorical. Such values are names, such as up, down and same. Normally anvi’o gives them its default colors in sorted order. This file says exactly which color each value gets instead, so that a color means the same thing across every figure in a paper. It also sets the order of the values.

Pass it with --reaction-value-colors for the reaction layer, and --compound-value-colors for the compound layer. The two layers are colored independently, so each can take its own file.

File format

Column	Required	Description
a value column	YES	The first column, which can be headed anything you like, such as value or status. Each row names one categorical value.
color	YES	A six-digit color hex code, such as #1f77b4. Color names are not accepted, since the colors that pathway maps reserve for their own unhighlighted elements are compared as hex codes.

Here is an example file:

status	color
up	#d62728
down	#1f77b4
same	#bcbd22

Every value of the layer needs a color. Anvi’o will not fill in the gaps with its default colors, since that would put colors you chose and colors chosen for you in one legend. Values in this file that the layer does not have are reported and ignored, so one file can serve several runs. Two values cannot share a color, since the maps and the legend could not tell them apart.

A value is a whole name, so a comma in it is just part of the name. This differs from a kegg-membership-colors-txt file, where a comma joins the names of a combination.

The order of the rows

The order of the rows is the order of the values. It is used in three places.

• The legend. The legend lists the values in this order, with the first value at the top.
• Drawing. Where map elements overlap, the first value is drawn on top. --reaction-reverse-overlay/--compound-reverse-overlay puts the last value on top instead.
• Choosing one value. Where several values meet, a rule chooses one. plurality_order gives a tie to the value that comes first, and order always takes the value that comes first. If up is in an earlier row than same, order chooses up for a map element whose KOs have both.

When this file does not apply

This file needs categorical values. It is refused unless the layer’s value type is categorical.

With a groups-txt, a layer whose file has a sample column also needs a rule in its sample summary, or this file is refused. That is --reaction-sample-summary for the reaction layer and --compound-sample-summary for the compound layer. Without a rule, each group’s map counts the group’s samples. No map then shows the values, so they take no colors, and there can be more than 18 of them without this file. A layer whose file has no sample column shows the same values on every group’s map, so this file is accepted for that layer without a rule.

Edit this file to update this information.