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Compare two cohorts with an interactive protein lollipop plot

Source: R/lollipop2.R
lollipopPlot2.Rd

Creates a mirrored GenomeSpy lollipop plot corresponding to maftools::lollipopPlot2(). Mutations from m1 are drawn above a shared protein model and mutations from m2 below it.

Usage

lollipopPlot2(
  m1,
  m2,
  gene = NULL,
  AACol1 = NULL,
  AACol2 = NULL,
  m1_name = NULL,
  m2_name = NULL,
  m1_label = NULL,
  m2_label = NULL,
  refSeqID = NULL,
  proteinID = NULL,
  labPosAngle = 0,
  labPosSize = 0.9,
  colors = NULL,
  pointSize = 1.2,
  showDomainLabel = TRUE,
  domains = NULL,
  proteinLength = NULL,
  count = c("events", "samples"),
  showLegend = TRUE,
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

m1, m2

maftools MAF objects or ordinary mutation data frames.

gene

One gene symbol.

AACol1, AACol2

Optional protein-change columns for m1 and m2.

m1_name, m2_name

Optional cohort names.

m1_label, m2_label

Amino-acid positions to label for each cohort, or "all".

refSeqID, proteinID

Optional RefSeq transcript or protein identifier selecting the shared protein model.

labPosAngle

Mutation-label angle in degrees. Positive values rotate counterclockwise, as in maftools.

labPosSize

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

colors

Optional named character vector overriding mutation-class colors.

pointSize

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

showDomainLabel

Draw ranged labels inside protein domains.

domains

Optional custom domain data frame with start, end, and label columns.

proteinLength

Optional protein length in amino acids.

count

Use mutation "events" (the maftools convention) or distinct tumor "samples" for recurrence heights.

showLegend

Show the mutation-class legend.

width, height

Widget dimensions.

elementId

Optional element ID.

Value

A MutGlyph htmlwidget.

Details

Both cohorts use one protein coordinate system and independently scaled recurrence axes. One cohort may contain no mutations for the selected gene.

Both stem sets extend to the center of the shared protein track, where the protein should cover their ends. GenomeSpy 0.84 cannot z-order complete children of a vconcat, so the later lower cohort currently draws its stems over the protein and looks somewhat ugly. A future GenomeSpy version with broader zindex support will render the intended layering without changing the plot geometry.

See also

lollipopPlot(), maftools::lollipopPlot2()

Examples

if (interactive()) {
  primary <- maftools::read.maf(
    system.file("extdata", "APL_primary.maf.gz", package = "maftools"),
    verbose = FALSE
  )
  relapse <- maftools::read.maf(
    system.file("extdata", "APL_relapse.maf.gz", package = "maftools"),
    verbose = FALSE
  )
  lollipopPlot2(
    m1 = primary,
    m2 = relapse,
    gene = "FLT3",
    AACol1 = "amino_acid_change",
    AACol2 = "amino_acid_change",
    m1_name = "Primary",
    m2_name = "Relapse",
    m1_label = 835,
    m2_label = 835
  )
}