lsn.transcripts.plot: Plot of Gene Lesions and Transcripts

In GRIN2: Genomic Random Interval (GRIN)

Plot of Gene Lesions and Transcripts

Description

The function can generate four types of lesion plots. (1) If the gene argument is specified, the function returns a gene-level plot showing all lesions affecting the gene, along with the transcript track and GRIN statistics. (2) If chrom, plot.start, and plot.end are specified, the function generates a locus-level plot for that genomic region, including the transcript track. If transTrack = FALSE, the function can return similar plots without the transcript track (useful for large regions such as chromosome bands or entire chromosomes). (3) If lesion.grp is specified, only lesions from that specific group will be shown in the plot. (4) If lesion.grp is not specified, all lesion types will be displayed for the given locus.

Usage

lsn.transcripts.plot(
  grin.res,
  gene = NULL,
  transTrack = TRUE,
  lsn.clrs = NULL,
  chrom = NULL,
  plot.start = NULL,
  plot.end = NULL,
  lesion.grp = NULL,
  spec.lsn.clr = NULL,
  extend.left = NULL,
  extend.right = NULL,
  expand = 5e-04,
  hg38.transcripts = NULL,
  hg38.cytoband = NULL
)

Arguments

grin.res	GRIN results (Output of the grin.stats() function).
gene	Gene symbol of interest.
transTrack	Logical; if FALSE, the transcript track will be excluded (useful for plots of large genomic regions such as entire chromosome arms or bands).
lsn.clrs	Optional named vector of lesion colors. If not provided, default colors from default.grin.colors() will be used.
chrom	Chromosome number. Required when plotting a locus (used with plot.start and plot.end).
plot.start	Start coordinate (in base pairs) of the locus of interest.
plot.end	End coordinate (in base pairs) of the locus of interest.
lesion.grp	Lesion group to include in locus plots. Only lesions from this group will be shown. Required when chrom, plot.start, and plot.end are specified.
spec.lsn.clr	Optional color for highlighting the lesion group of interest in locus plots.
extend.left	Optional numeric value to extend the left side of the transcripts track (for alignment adjustments).
extend.right	Optional numeric value to extend the right side of the transcripts track (for alignment adjustments).
expand	Numeric; controls the proportion of upstream and downstream regions included in the plot relative to gene coordinates. Default is 0.0005. Set to 0 to plot the gene region only.
hg38.transcripts	Transcripts data from AnnotationHub (hg38, version 110). Required if transTrack = TRUE.
hg38.cytoband	Data frame of hg38 cytogenetic bands (start and end coordinates in base pairs).

Details

The function returns a plot that displays lesions affecting either a gene or a user-defined genomic region. When plotting a gene:

• The top panel shows all transcripts of certain gene or group of genes in a small region retrieved from Ensembl if transTrack=TRUE (default).

• The middle panel visualizes lesions affecting the gene or locus, color-coded by type.

• The bottom panel presents GRIN statistics, including the number of affected subjects, -log10(p), and -log10(q) values in case of gene plots.

When plotting a genomic locus (via chrom, plot.start, plot.end):

• Only the transcripts track (if transTrack = TRUE) and lesion panel are shown.

• GRIN statistics are omitted.

For large regions like cytobands or entire chromosomes, set transTrack = FALSE to avoid overcrowding from long transcript tracks.

Value

A multi-panel plot showing:

• Lesions and transcripts for a gene (with GRIN statistics), or

• Lesions and optional transcripts for a genomic locus, or

• Lesions alone for large genomic regions if transcripts and GRIN panels are excluded.

Author(s)

Abdelrahman Elsayed [e-mail] and Stanley Pounds [e-mail]

References

Cao, X., Elsayed, A. H., & Pounds, S. B. (2023). Statistical Methods Inspired by Challenges in Pediatric Cancer Multi-omics.

See Also

grin.stats

Examples

data(lesion_data)
data(hg38_gene_annotation)
data(hg38_chrom_size)
data(hg38_cytoband)

# run GRIN analysis using grin.stats function
grin.results=grin.stats(lesion_data,
                        hg38_gene_annotation,
                        hg38_chrom_size)

# Plots Showing Different Types of Lesions Affecting a region of Interest without plotting the
# transcripts track (this will allow plotting a larger locus of the chromosome such as a
# chromosome band (should specify transTrack = FALSE):
cdkn2a.locus=lsn.transcripts.plot(grin.results, transTrack = FALSE,
                                   hg38.cytoband=hg38_cytoband, chrom=9,
                                   plot.start=19900000, plot.end=25600000,
                                    lesion.grp = "loss", spec.lsn.clr = "blue")

 # Plots Showing Different Types of Lesions Affecting the whole chromosome:
 chrom.plot=lsn.transcripts.plot(grin.results, transTrack = FALSE,
                                 hg38.cytoband=hg38_cytoband, chrom=9,
                                 plot.start=1, plot.end=141000000)

GRIN2 documentation built on June 17, 2025, 9:11 a.m.