kegg-slice-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 slices of the reaction elements drawn on kegg-pathway-map files, or the slices of the rings that color their borders.

With --reaction-slice-by, a box or line that stands for several KOs, KEGG reactions, or genes is drawn in slices, one for each accession or gene with a value on the map. Slices are too narrow to label, and a box label names only the first KO of the element. This table says what each slice stands for. The program writes it as slice_key_reactions.txt at the top of the output directory, beside the colorbars. One file covers every map of the run. Options that arrange the map files, such as --categorize-files and --collate-files-by-map, do not move it. See anvi-draw-kegg-pathways for how slices are drawn and how their shares are found.

With --reaction-border-slice-by, the ring that colors the border of a box is divided among the accessions or genes with border values. The program then writes a second table of the same form, slice_key_reactions_border.txt, beside the first. It lists the slices of the rings, as described in Slices of rings.

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. The one map drawn from a kegg-reaction-txt without a sample column is unified.
entry_id	The ID of the element’s entry in the map’s KGML file.
x	The x coordinate of the element in the map’s KGML file. For a box, this is its center. For a line, this is the point near the middle of its first piece where Biopython puts the label of a line.
y	The y coordinate of the same point.
label	The label of the element in the KGML file, such as K01623....
slice	The position of the slice, counting from 1. The slices of a box count from the left. The slices of a line count from its first point in the KGML file, within each cycle of dashes. This is blank for an element drawn whole for a reason.
accession	The KO or KEGG reaction that the slice stands for. For a slice of a gene (--reaction-slice-by gene), this lists the gene’s KOs or KEGG reactions in the element, in KGML order, joined by commas without spaces, such as K01623,K01624. These are the accessions of the element for which the gene has rows anywhere in the file, so a gene has the same label on every map. On a map where the gene has rows for only some of them, all are still listed.
gene_id	The gene that the slice stands for, with --reaction-slice-by gene. This is blank for a slice of an accession.
value	The value of the accession or gene on the drawn map. This is a number, or a categorical value with --reaction-value-type categorical. A gene with rows for two or more accessions of the element takes the mean of these rows in a sample by default. On the map of a group or the unified map, the value is the summary of the values in the samples or groups.
share	The share of the element’s width or length that the slice takes. The shares of an element on a drawn map sum to 1.
color	The color of the slice, as a hex code. For an element drawn whole, it is the color of the whole element.
drawn_whole	Blank for a slice that is drawn. For an element drawn whole, it gives the reason, over the cap for a box or line too short for a line. A ring can also be drawn whole for the reason fill not sliced.

Rows

Each row is one slice on one drawn map. An element on the unified map and on the maps of three samples has rows for each of the four maps. Its slices can differ from map to map, since an accession or gene gets a slice only on the maps where it has a value. The same position can then hold different accessions or genes on different maps.

An element with one slice is drawn whole in the color of that slice. It has one row, with slice 1 and share 1.0.

An element with more slices than fit is drawn whole in the color of a stand-in value. A box is drawn whole where a slice of equal width would be narrower than 8 points. In a layer with a border column, the slices of a box fit inside its ring, which leaves 85 of its 92 points. A line is drawn whole where any of its pieces would give a slice of equal length shorter than the line is wide. Only the part of the piece that compound circles leave visible counts. Such an element has a row for each slice it would have had. These rows have a blank slice, the share and value that each slice would have had, and the color of the whole element. drawn_whole gives the reason. The stand-in value itself is not listed.

Elements left uncolored have no rows. These include an element whose slices with values all have a weight of 0, and an element drawn whole whose stand-in value is undefined.

The rows are sorted by map, then by drawn_map, then by entry ID, and then by slice. 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. The file is written whenever slicing is on. It holds only the header if no slice was drawn.

Examples

Here are rows for one box of map 00010, drawn in equal slices on the maps of two samples. The box has two slices on the map of SAMPLE_1. On the map of SAMPLE_2, only K16306 has a value, so it fills the box.

map	drawn_map	entry_id	x	y	label	slice	accession	gene_id	value	share	color	drawn_whole
00010	SAMPLE_1	18	966	814	K01623…	1	K01622		36.5	0.5	#a01a9c
00010	SAMPLE_1	18	966	814	K01623…	2	K16306		15.5	0.5	#f79143
00010	SAMPLE_2	18	966	814	K01623…	1	K16306		30.5	1.0	#c13b82

Here are rows for the same box from a run sliced by gene, on the maps of two other samples, control and treated. The rows come from the example file for slices of genes in anvi-draw-kegg-pathways. gene_1 has rows for K01623 and K01624, so it is one slice. On the map of treated, its rows are 1.2 for K01623 and 0.8 for K01624, so its value is their mean, 1.0. gene_2 has a row for K01623 only.

map	drawn_map	entry_id	x	y	label	slice	accession	gene_id	value	share	color	drawn_whole
00010	control	18	966	814	K01623…	1	K01623,K01624	gene_1	0.2	0.5	#db5c68
00010	control	18	966	814	K01623…	2	K01623	gene_2	0.5	0.5	#a31e9a
00010	treated	18	966	814	K01623…	1	K01623,K01624	gene_1	1.0	0.5	#0d0887
00010	treated	18	966	814	K01623…	2	K01623	gene_2	-0.4	0.5	#f0f921

Here are the first three of the 14 rows of a box drawn whole, from a run without samples. The box would have had 14 slices, which is more than the 11 that fit. The whole box takes one color.

map	drawn_map	entry_id	x	y	label	slice	accession	gene_id	value	share	color	drawn_whole
00190	unified	255	960	772	K00234…		K00234		16.5	0.09090909090909091	#c33d80	over the cap
00190	unified	255	960	772	K00234…		K00235		7.5	0.12121212121212122	#c33d80	over the cap
00190	unified	255	960	772	K00234…		K00236		21.5	0.030303030303030304	#c33d80	over the cap

Slices of rings

The table of the slices of rings, slice_key_reactions_border.txt, has the same columns. value and color are those of the border column, and drawn_whole gives why a ring is drawn whole. The rings of a run are either aligned with the slices of the fill or divided on their own, and the positions and shares depend on which.

• Aligned with the fill. Where --reaction-slice-by and --reaction-border-slice-by name the same unit, each column of the fill takes the border value of its own accession or gene, as bands above and below it. A row lists such a column. Its slice and share are those of the column in slice_key_reactions.txt. A column without a border value has no row.
• Divided on its own. Otherwise, each ring is divided among its accessions or genes with border values. The slices count clockwise from the top left corner of the box, and share is the share of the ring that a slice takes.

A ring of one slice is drawn whole in the color of that slice, with slice 1 and share 1.0. Rings can also be drawn whole for these reasons, in the color of a stand-in value:

• over the cap. An aligned ring is drawn whole where its fill has more slices than fit. Its rows list the units with both a slice of the fill and a border value, with the shares of the fill. A ring divided on its own is drawn whole where it would have more than 11 slices.
• fill not sliced. An aligned ring is drawn whole where the fill of its box is not sliced, since the map shows presence or the box has no fill value there. Its rows list every unit with a border value, with equal shares.

Rings left out have no rows. These include a ring whose slices with values all have a weight of 0, and a ring drawn whole whose stand-in value is undefined.

Here are rows of the aligned rings of the box of the first example, on the map of SAMPLE_1. The fill was sliced by KO, with shares from a column of weights, and the border column holds the categorical values up and down.

map	drawn_map	entry_id	x	y	label	slice	accession	gene_id	value	share	color	drawn_whole
00010	SAMPLE_1	18	966	814	K01623…	1	K01624		up	0.47619047619047616	#d62728
00010	SAMPLE_1	18	966	814	K01623…	2	K01622		down	0.047619047619047616	#1f77b4
00010	SAMPLE_1	18	966	814	K01623…	3	K16306		up	0.47619047619047616	#d62728

Here are rows of the same box on the unified map of that run, where the fills show presence. The fill is not sliced, so the ring is whole. Its color is that of up, which plurality_order chooses among the three KOs.

map	drawn_map	entry_id	x	y	label	slice	accession	gene_id	value	share	color	drawn_whole
00010	unified	18	966	814	K01623…		K01624		up	0.3333333333333333	#d62728	fill not sliced
00010	unified	18	966	814	K01623…		K01622		down	0.3333333333333333	#d62728	fill not sliced
00010	unified	18	966	814	K01623…		K16306		up	0.3333333333333333	#d62728	fill not sliced

Edit this file to update this information.