Skip to main content

Rows

Auto-generated from the config schema in the source — see the config guide for concepts. Built into JBrowse core. View source.

The rows setting of the displays that draw one row per value of a field, with the dendrogram sidebar beside them: a RowArrangement plus the field, filter, which narrows the rows by attribute, and an axis with grid. A string is the field; the arrangement members name rows by value of the field, so a write changing it clears them.

Example usage

{ type: 'LinearWiggleDisplay', rows: 'source' }
{ type: 'LinearMultiRowFeatureDisplay', rows: 'sample' }
{
  type: 'LinearWiggleDisplay',
  rows: { field: 'source', sort: ['tumor', 'normal'], labels: { tumor: 'Tumor' } },
}

Config slots

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
field
featureField = ''		The field whose values each take a row. Writing rows: "source" sets this slot. Empty is the display's default: no rows on the quantitative display, and a field picked off the data on the multi-row feature display.
filter
RowPredicate		The rows shown by attribute: a list of RowPredicate entries over a row attribute, each one a row must pass: a samplesTsv column on the variant display ([{ field: 'population', oneOf: ['EUR', 'AFR'] }]), a subtrack's field such as group on wiggle, and group, which rows.groups derives, on the mark displays. 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.
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.
Inherited from RowArrangement6 slots
sort
stringArray of strings or numbers = []		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.
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.
kept
stringArray of strings or numbers = []		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.