A named list of options to configure the plot. Available options:
- crossingWeight
Weight for tentacle bundles between two pairs of samples crossing each other. Defaults to 10
.
- pathLengthWeight
Weight for the total length of the paths (tentacle bundles) connecting samples. Defaults to 2
.
- orderMismatchWeight
Weight for the mismatch in the order of samples. The order is based on the "phylogenetic center of mass" computed from the subclonal compositions. Defaults to 2
.
- bundleMismatchWeight
Weight for the mismatch in the placement of bundles. The "optimal" placement is based on the subclonal compositions, but such placement may produce excessively long tentacle bundles. Defaults to 3
.
- divergenceWeight
Weight for the sum of divergences between adjacent samples. Defaults to 4
.
- bellTipShape
The shape of the bell tip. 0 is a sharp tip, 1 is a blunt tip. Defaults to 0.1
.
- bellTipSpread
How much to spread nested bell tips. 0 is no spread, 1 is full spread. Defaults to 0.5
.
- bellStrokeWidth
The width of strokes in the bell. Defaults to 1
.
- bellStrokeDarkening
How much the stroke color of the bells is darkened. Defaults to 0.6
.
- bellPlateauPos
Where the bell has fully appeared and the plateau starts. Defaults to 0.75
.
- sampleHeight
Height of real sample nodes Defaults to 110
.
- sampleWidth
Width of sample nodes Defaults to 90
.
- inferredSampleHeight
Height of inferred sample nodes Defaults to 120
.
- gapHeight
Height of gaps between samples. Gaps are routes for tentacle bundles. Defaults to 60
.
- sampleSpacing
Vertical space between samples Defaults to 60
.
- columnSpacing
Horizontal space between columns Defaults to 90
.
- tentacleWidth
Width of tentacles in pixels Defaults to 2
.
- tentacleSpacing
Space between tentacles in a bundle, in pixels Defaults to 5
.
- inOutCPDistance
Relative distance of tentacle control points from the edge of the sample node Defaults to 0.3
.
- bundleCPDistance
Relative distance of tentacle bundle's control points. The higher the value, the longer the individual tentacles stay together before diverging. Defaults to 0.6
.
- sampleFontSize
Font size for sample labels Defaults to 12
.
- showLegend
Whether to show the legend Defaults to TRUE
.
- phylogenyColorScheme
Whether to use a color scheme based on phylogeny Defaults to TRUE
.
- phylogenyHueOffset
Offset for the hue of the phylogeny color scheme. If the automatically generated hues are not to your liking, you can adjust the hue offset to get a different color scheme. Defaults to 0
.
- sampleTakenGuide
Type of the "sample taken" guide. "none"
for no guides, "line"
for a faint dashed line in all samples, "text"
same as line, but with a text label in one of the samples. "text-all"
same as text, but with a text label in all samples. Defaults to "text"
.
- showRankTitles
Whether to show rank titles above the samples (if provided). Defaults to TRUE
.
- normalsAtPhylogenyRoot
Whether the root of the phylogenetic tree contains normal cells. If true, no tentacles will be drawn for the root clone and its color will be white if phylogenyColorScheme is used. Defaults to FALSE
.