Draw an interactive protein lollipop plot

Creates a GenomeSpy protein-mutation lollipop plot from a maftools MAF object or an ordinary data frame. The basic layout follows maftools::lollipopPlot(), while the displaced layout separates dense hotspots and connects every marker back to its true protein position.

Usage

lollipopPlot(
  maf,
  data = NULL,
  gene = NULL,
  AACol = NULL,
  labelPos = NULL,
  labPosSize = 0.9,
  showMutationRate = TRUE,
  showDomainLabel = TRUE,
  refSeqID = NULL,
  proteinID = NULL,
  colors = NULL,
  domains = NULL,
  proteinLength = NULL,
  layout = c("basic", "displaced"),
  count = c("events", "samples"),
  minCount = NULL,
  yScale = NULL,
  showLegend = TRUE,
  collapsePosLabel = TRUE,
  labPosAngle = 0,
  pointSize = 1.5,
  topPadding = NULL,
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

maf

A maftools MAF object.

data

Optional mutation data frame, following maftools::lollipopPlot(). MutGlyph accepts its two-column position/count convention as well as named position, mutation, variant_class (or classification), sample, gene, and count columns.

gene

One gene symbol. Required for MAF input; optional when a custom data frame contains exactly one value in its gene column.

AACol

Optional column containing protein changes. With MAF input, HGVSp_Short, Protein_Change, and AAChange are tried in that order.

labelPos

Amino-acid positions to label, or "all". The displaced layout labels all mutations by default; the basic layout labels none.

labPosSize

Relative mutation-label size, matching maftools' cex semantics.

showMutationRate

Include the mutated-sample fraction in the title.

showDomainLabel

Draw ranged labels inside protein domains.

refSeqID, proteinID

Optional RefSeq transcript or protein identifier. These retain maftools' domain-selection semantics. If compatible RefSeq metadata is present in the mutation input, MutGlyph warns about mixed or mismatching isoforms without silently filtering mutations.

colors

Optional named character vector overriding mutation-class colors.

domains

Optional custom domain data frame with start, end, and label columns. description and protein_length are optional.

proteinLength

Optional protein length in amino acids.

layout

Either "basic" for true-position vertical lollipops or "displaced" for collision-aware markers, labels, and connectors.

count

Use mutation "events" (the maftools convention) or distinct tumor "samples" for recurrence heights. For a pre-aggregated data frame, this also defines what its count column represents.

minCount

Minimum plotted recurrence under the selected count mode. When NULL, the basic layout uses one and the displaced layout uses two.

yScale

"linear" or "log". When NULL, basic plots use linear and displaced plots use logarithmic scaling.

showLegend

Show the mutation-class legend.

collapsePosLabel

Combine mutation labels at the same amino-acid position, for example D835Y/H. Used by the basic layout.

labPosAngle

Mutation-label angle in degrees. Positive values rotate counterclockwise, as in maftools. Used by the basic layout.

pointSize

Relative marker-size multiplier, matching maftools' linear cex semantics.

topPadding

Vertical space in pixels reserved above the mutation panel for mutation labels. When NULL, the basic layout uses 10 pixels and the displaced layout uses 70 pixels.

width, height

Widget dimensions.

elementId

Optional element ID.

Value

A MutGlyph htmlwidget.

Details

With MAF input and no domains, protein domains are read from maftools' bundled protein_domains.RDs snapshot. Custom data without domains is drawn against a plain protein backbone. mutglyph_interpro_domains() returns a compatible domain table when online InterPro annotations are desired. When no identifier is supplied, MutGlyph follows maftools by selecting the longest bundled protein model (and the first transcript when lengths tie). Selected transcript and protein identifiers are shown below the plot title.

Mutation event and distinct-sample counts are both retained in plot$x$spec$datasets$mutations, irrespective of which one is plotted.

See also

oncoplot(), rainfallPlot(), and as_json().

Examples

if (interactive()) {
  laml <- maftools::read.maf(
    maf = system.file("extdata", "tcga_laml.maf.gz", package = "maftools"),
    verbose = FALSE
  )
  # Frozen InterPro representative-domain matches for UniProt P36888.
  # Fetch current matches with mutglyph_interpro_domains("P36888").
  flt3_domains <- data.frame(
    start = c(246, 438, 564, 756),
    end = c(357, 531, 695, 958),
    label = c("Ig-like", "Ig-like", "Kinase N", "Kinase C"),
    protein_length = 993
  )
  lollipopPlot(
    laml,
    gene = "FLT3",
    AACol = "Protein_Change",
    domains = flt3_domains,
    layout = "displaced"
  )
}