GRIN2 (version 2.0.0)

lsn.transcripts.plot: 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
)

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.

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).

Author

Abdelrahman Elsayed and Stanley Pounds

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.

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

# \donttest{
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)
# }