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VariantRows

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the variants plugin. View source.

The variant display's rows: one per sample, or with field: 'haplotype' one per phased haplotype, with the RowsWithStep arrangement, axis and row height.

Example usage

{ type: 'LinearVariantDisplay', rows: { sort: ['HG002'], step: 10 } }
{ type: 'LinearVariantDisplay', rows: 'haplotype' }

Config slots

A setting written to it names members one by one: a member left out stays as it is, and null resets one. One that changes field first clears sort, labels, tree, kept, colors, which name the old values, except those it states. A write between haplotype and sample clears nothing, since a haplotype row answers to its sample's name. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

SlotDescription
filter
RowPredicate		The rows shown by attribute: a list of RowPredicate entries over a samplesTsv column, each one a row must pass, as [{ field: 'population', oneOf: ['EUR', 'AFR'] }]. A row missing the attribute fails every test but valid: false. It narrows the rows before kept, and a write changing field keeps it, since it names no row by its value; a row's name goes in kept.
field
stringEnum (sample, haplotype) = 'sample'		What one row is: sample, a row per sample colored by its allele dosage, or haplotype, a row per phased haplotype of each sample, named "<sample> HP1", "<sample> HP2". That number is JBrowse's, counting a sample's alleles from 1, not the VCF's HP tag. A haplotype row answers to its sample's name, so a sort, labels, colors, tree or kept entry naming a sample reaches its haplotype rows, and switching between the two keeps them: a haplotype entry waits unseen in sample mode, and a sample ranks at its first haplotype entry. A haplotype row's label is its own labels entry exactly, else its sample's label and its haplotype (Mother HP1), and a haploid sample's one row takes the sample's label alone.
Inherited from RowsWithStep1 slot
step
number = 'fit'		Row height in px: the px from one row's top to the next, the rows that do not fit scrolling; or "fit", the default, dividing the track's height between the rows, as heightMode: "fit" does on a feature track. The track never grows to hold its rows. Vega-Lite's word for a band's size, as in height: { step }.
Inherited from Rows3 slots
axis
RowAxisWithGrid		The guide down the left of the rows, a RowAxisWithGrid: whether the tree and the row names draw, the sidebar's width, and a line between rows. What it draws is rows.tree and rows.labels.
colors
stringMap = {}		A color pinned on a row, by name, over whatever rows.color maps it to, as labels pins its text: ggplot2's scale_*_manual(values = c(name = ...)). The arrangement dialog's row swatches write it. A row with none takes rows.color, else the file's own color (MAF's samples[].color, a listed source's color), else the palette where the rows share one panel.
color
RowColor		The rows colored by an attribute: a RowColor channel from a row field through a scale, name (each row) by default. Per-row colors are rows.colors, which win over it.
Inherited from RowArrangement4 slots
sort
stringArray = []		The row order, as Vega-Lite's sort lists it: the rows listed lead, in this order, and none is dropped. The rest keep the order their source lists them in (a VCF's samples, a multi-BigWig's subtracks), or sort, digits by magnitude, where the rows are values found on features. A clustering run, the arrangement dialog and "Sort rows here" all write it, and a run rotates its dendrogram towards it rather than discarding it.
labels
stringMap = {}		A label drawn beside a row in place of its name, by name. Whether any label draws is rows.axis.labels.
tree
RowTree		The dendrogram beside the rows, a RowTree: newick, or { newick, provenance } where a clustering run wrote it beside the order it produced. A reorder that moves a row drops it. Whether it draws is rows.axis.tree. The rows follow the tree's leaves, then rows.sort for any rows the tree lacks; a supplied tree rotates towards rows.sort, so a sort also decides which way each clade faces.
kept
stringArray = []		The rows shown, by name: a clade picked off the tree, or the rows one key row stands for. It narrows the rows to those it names, after filter where the display declares one; empty shows every row, and a list naming no current row shows none, with a notice. Keyed: a write changing field clears it.