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MafRows

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

The MAF display's rows: one per species (or genome) the alignment holds, and a copy row (mm10~2) where a block aligns one twice. The object is the RowArrangement a reader gives the rows, each member by row name, with the colors pinned on rows and an axis with no grid, since the species rows keep a gap instead. A row is always a species, so it takes no field, and writing it changes only the members stated.

Example usage

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

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
axis
RowAxis		The guide down the left of the species rows, a RowAxis: the species tree and each species' name.
colors
stringMap = {}		A color pinned on a row, by name, over whatever rows.color maps it to, as labels pins its text. The arrangement dialog's row swatches write it. A row with none takes rows.color, else the adapter's samples[].color, else the palette. A copy row takes its species'.
color
RowColor		The rows colored by an attribute: a RowColor channel, 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.