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RowArrangement

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 a display whose rows are not the values of a field: the MAF display's species rows. It holds the arrangement a reader gives the rows, which every product writes as a session edit to this object: the order, the labels, the pinned colors, the tree and the focus, each by row name; beside them color, the rows colored by an attribute, and axis, the guide that draws the tree and the names. Writing it changes only the members stated. Rows is this plus the field whose values each take a row.

Example usage

{
  type: 'LinearMafDisplay',
  rows: { sort: ['mm10', 'hg38'], labels: { mm10: 'Mouse' }, axis: { tree: false } },
}

Config slots

A setting written to it names members one by one: a member left out stays as it is, and null resets one. 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
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.
axis
RowAxis		The guide down the left of the rows, a RowAxis: whether the tree and the row names draw, and the sidebar's width. What it draws is rows.tree and rows.labels.
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.