Interactive, zoomable GISTIC copy-number landscapes in R

gisticChromPlot() is an interactive counterpart to maftools::gisticChromPlot(). Amplifications grow upward, deletions grow downward, and a compact chromosome strip keeps the two profiles aligned while the shared genomic scale is zoomed or panned. This makes it possible to move from the genome-wide copy-number landscape into a narrow amplification or deletion peak without redrawing the plot.

Read standard GISTIC output

MutGlyph accepts the same GISTIC object produced by maftools::readGistic(). This example uses the small TCGA acute myeloid leukemia GISTIC result bundled with maftools.

library(MutGlyph)

gistic <- maftools::readGistic(
  gisticDir = system.file("extdata", package = "maftools"),
  isTCGA = TRUE,
  verbose = FALSE
)

gisticChromPlot(gistic, height = 300)

Try the plot: Scroll or pinch to zoom into a GISTIC peak, drag to pan, and hover over intervals for genomic coordinates, G-scores, q-values, and alteration frequencies.

The two profiles use the same G-score domain, making amplification and deletion magnitudes directly comparable. Intervals passing fdrCutOff are drawn with the amplification or deletion color; other intervals use an opaque context color. Drawing every interval exactly once avoids alpha-blending artifacts where narrow rectangles overlap. By default, the five significant cytobands with the lowest q-values are labelled.

Choose bands and styling

Use markBands = "all" to label every significant cytoband, or supply selected names. The familiar maftools arguments retain their usual meaning where they fit the interactive composition.

Custom genomic annotations are supplied as a regular data frame. Here the narrowest high-scoring intervals overlap KMT2A and ERG. The coordinates below are the corresponding NCBI RefSeq gene ranges on GRCh37/hg19 (KMT2A, ERG). Labels are placed at the highest G-score interval overlapping each range.

gene_annotations <- data.frame(
  chromosome = c("chr11", "chr21"),
  start = c(118307207, 39739183),
  end = c(118397547, 40033707),
  label = c("KMT2A", "ERG"),
  event_type = c("Amp", "Amp")
)

gisticChromPlot(
  gistic,
  fdrCutOff = 0.05,
  markBands = c("5q31.2", "7q32.3", "17q11.2"),
  annotations = gene_annotations,
  color = c(Amp = "#E45756", Del = "#4C78A8"),
  nonSignificantColor = "lightgray",
  height = 300
)

Hovering over a score interval reports its genomic coordinates, G-score, q-value, mean amplitude, and alteration frequency. Cytoband labels provide peak-level q-values and sample and gene counts. Only these compact score and summary fields are embedded; the large sample-level lesion matrix is omitted from the HTML widget.

Use a genomic axis at close zoom levels

The chromosome strip gives useful whole-genome context but becomes less useful when zooming into a small interval. Set chromosomeTrack = "axis" to omit the strip and place a regular zoom-aware genomic axis below the deletion profile.

gisticChromPlot(
  gistic,
  chromosomeTrack = "axis",
  region = "chr21:5,000,000-48,000,000",
  height = 300
)