kegg-label-key-txt

A TXT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Provided by

anvi-draw-kegg-pathways

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.

Description

This artifact is a TAB-delimited text file written by anvi-draw-kegg-pathways. It lists the reaction boxes drawn without their labels on kegg-pathway-map files, because of the bars inside them.

With --reaction-bar-column, a map whose bar scale has values on both sides of 0 draws bars that grow both ways from a gray zero line. The label of a box fills its upper half, where it would hide the zero line and the ends of short bars, so the boxes of the default fill style are drawn without their labels. A box whose bar runs up its height is drawn without its label too, since the top of its bar would run behind the label. Bars run up their boxes with --reaction-bar-orientation vertical, and by default in boxes sliced with --reaction-slice-by whose accessions or genes have two or more bar values. This table says what each of these boxes stands for. The program writes it as label_key_reactions.txt at the top of the output directory, beside the bar keys. One file covers every map of the run. It is written where the bars are vertical, or where the bar scale of the unified map, or the scale shared by the maps of the samples or groups, has values on both sides of 0. Boxes of the strip style keep their labels, so a run of strips writes no table. See anvi-draw-kegg-pathways for how bars are drawn.

File format

The file has a header line and these columns:

Column	Description
map	The number of the KEGG map, such as 00010.
drawn_map	Which map of that KEGG map was drawn. This is unified for the unified map, or the name of a sample or group for the map of that sample or group. A kegg-reaction-txt without a sample column draws only the unified map, unless a kegg-compound-txt with a sample column draws maps of samples too. Its boxes are then the same on every map, and each map lists them.
entry_id	The ID of the box’s entry in the map’s KGML file.
x	The x coordinate of the center of the box in the map’s KGML file.
y	The y coordinate of the center of the box.
label	The label of the box in the KGML file, such as K01623.... This is the label that was not drawn.
accession	The KOs or KEGG reactions of the box that the file has on the drawn map, in KGML order, joined by commas without spaces, such as K01622,K16306. On the map of a sample, these are the accessions with rows in that sample. On the map of a group or the unified map, they are those of any of its samples. A file without a sample column gives every map all of its accessions.
bar	The bar value of the box on the drawn map. On the map of a group or the unified map of a file with a sample column, it is the summary of the bar values in the samples or groups. It is blank for a box drawn in columns with --reaction-slice-by, whose bar values the kegg-slice-key-txt gives slice by slice. A sliced box drawn whole lists the one bar it shows, such as the mean of the bar values of its slices, weighted by their shares.

Rows

Each row is one box on one drawn map. The rows are sorted by map, then by drawn_map, then by entry ID. The unified map comes first, and the maps of the samples or groups follow in the order in which they are drawn. Rows name maps, not files. A map drawn only as a panel of a grid is listed under its sample or group, like any other.

A box is listed on a drawn map only where its bar is vertical or its bar scale has values on both sides of 0. The unified map and the maps of the samples or groups have bar scales of their own, so a box can be listed on one and labeled on the other. A box left uncolored for want of a bar value keeps its label and is not listed. Boxes are listed whether or not --reaction-labels labels standard maps.

Examples

Here are rows for three boxes of map 00010, from a file of log ratios in three samples, with --reaction-bar-sample-summary mean. The bar scale of the unified map runs from -1 to 3.5, and the scale shared by the maps of the samples from -1 to 5. On the unified map, the box of entry 18 shows the mean of its bar values across the samples. On the map of SAMPLE_1, only two of its KOs have rows.

map	drawn_map	entry_id	x	y	label	accession	bar
00010	unified	18	966	814	K01623…	K01624,K01622,K16306	3.4166666666666665
00010	unified	61	916	968	K00134…	K00134	-0.5
00010	unified	159	1148	1592	K01007	K01007	-1.0
00010	SAMPLE_1	18	966	814	K01623…	K01622,K16306	2.75

Edit this file to update this information.