lsn.transcripts.plot: Plot Genomic Lesions with Transcript Annotations
In GRIN2: Genomic Random Interval (GRIN)
View source: R/lsn.transcripts.plot.R
lsn.transcripts.plot R Documentation
Plot Genomic Lesions with Transcript Annotations
Description
Creates an integrated genomic-region plot combining patient-level genomic
lesions with optional transcript annotations, chromosome context, genomic
coordinates, lesion-type legends, and gene-level GRIN2 statistics.
The function supports both gene-centered plots and user-defined genomic
regions. Single-position lesions, or lesion types explicitly selected by the
user, are drawn at their exact genomic coordinates with user-controlled
marker size.
Usage
lsn.transcripts.plot(
grin.res,
gene = NULL,
chrom = NULL,
plot.start = NULL,
plot.end = NULL,
transTrack = TRUE,
show.ideogram = TRUE,
show.axis = TRUE,
show.transcript.labels = FALSE,
transcript.mode = c("all", "selected"),
selected.transcript = NULL,
lesion.grp = NULL,
lsn.clrs = NULL,
spec.lsn.clr = NULL,
point.lesion.groups = NULL,
point.size.mm = 0.8,
expand = 0.0005,
hg38.transcripts = NULL,
hg38.cytoband = NULL,
genome = "hg38",
transcript.height = 0.31,
draw = TRUE
)
Arguments
grin.res
A GRIN2 results object containing at least lsn.data.
Gene-centered plots additionally require gene.data; gene-level recurrence
and constellation statistics are displayed when gene.hits is available.
gene
Optional character scalar specifying the gene to plot. When
supplied, genomic coordinates are obtained from grin.res[["gene.data"]].
chrom
Chromosome for a user-defined regional plot. Used only when
gene = NULL. Values with or without the chr prefix are accepted.
plot.start, plot.end
Numeric start and end coordinates for a
user-defined regional plot. Both are required when gene = NULL.
transTrack
Logical; whether to display transcript annotations.
show.ideogram
Logical; whether to display a chromosome ideogram.
show.axis
Logical; whether to display a genomic-coordinate axis.
show.transcript.labels
Logical; whether transcript or gene labels are
displayed within the transcript track.
transcript.mode
Character string specifying which transcript
annotations to display. Use "all" for all overlapping transcripts or
"selected" for transcript IDs supplied through selected.transcript.
selected.transcript
Character vector of transcript IDs retained when
transcript.mode = "selected". Version suffixes are ignored during
matching, allowing identifiers such as ENST00000342505 and
ENST00000342505.8 to match.
lesion.grp
Optional character vector specifying lesion types to plot.
lsn.clrs
Optional named character vector assigning colors to lesion
types. Vector names must match the lesion-type values in
grin.res[["lsn.data"]]$lsn.type. If an unnamed vector is supplied, it
must contain exactly one color for each plotted lesion type. When
lsn.clrs = NULL, colors are assigned automatically.
spec.lsn.clr
Optional color used when a single lesion type is
selected through lesion.grp.
point.lesion.groups
Optional character vector specifying lesion types
to display as point markers. When NULL, each lesion is classified from
its genomic coordinates: lesions with identical start and end coordinates
are displayed as circles, whereas lesions spanning multiple positions are
displayed as intervals.
point.size.mm
Positive numeric scalar specifying the diameter, in
millimeters, of lesions displayed as circles. The default is 0.8.
expand
Non-negative numeric proportion used to expand a gene-centered
plotting interval upstream and downstream. It is ignored for user-defined
regional plots, which use the supplied coordinates exactly.
hg38.transcripts
An EnsDb transcript-annotation object compatible
with ensembldb::getGeneRegionTrackForGviz(). Required when
transTrack = TRUE. A compatible GRCh38 transcript annotation can be
obtained through AnnotationHub using the workflow shown in the examples.
hg38.cytoband
Cytoband annotation supplied to
Gviz::IdeogramTrack(). Required when show.ideogram = TRUE. A GRCh38
cytoband annotation is provided with GRIN2 as hg38_cytoband and can be
loaded using data(hg38_cytoband).
genome
Genome identifier passed to the Gviz annotation tracks.
transcript.height
Relative vertical space allocated to the transcript
annotation track. Increasing this value provides additional space when
many transcripts are displayed. This value is used only when
transTrack = TRUE.
draw
Logical; if TRUE, draw the assembled plot on a new graphics
page. The plot object is returned invisibly in either case.
Details
In gene mode, the displayed interval is derived from the matching entry in
gene.data and can be expanded using expand. In regional mode, the exact
interval specified by chrom, plot.start, and plot.end is used.
Transcript annotations can be shown in full or restricted to selected
transcript IDs. Selected IDs are matched after removal of version suffixes.
Unmatched IDs are reported in a warning when at least one requested
transcript is available; the function stops with an informative error when
none of the requested transcripts can be found.
Point-like lesions are plotted at their exact genomic start coordinates and
use physical marker sizes measured in millimeters. Lesions are ordered first
by lesion type and then by interval size, with source order used to break
exact ties.
When transcript annotations are not displayed, the vertical space allocated
to the ideogram and genomic-coordinate axis is reduced automatically so that
the lesion panel occupies the available plotting area more efficiently.
For gene-centered plots, available lesion-specific subject counts and
transformed p- and q-values are displayed together with ordered
constellation statistics from gene.hits. Missing statistics are omitted
rather than preventing plot construction.
Value
Invisibly returns a gtable/grob object representing the assembled
figure. When draw = TRUE, the figure is also drawn.
See Also
grin.stats(), Gviz::GeneRegionTrack(),
Gviz::GenomeAxisTrack(), Gviz::IdeogramTrack(),
ensembldb::getGeneRegionTrackForGviz()
Examples
data("grin.results")
data("hg38_cytoband")
# Plot lesions across a user-defined genomic region without transcript
# annotations. This example uses only data included with GRIN2.
lsn.transcripts.plot(
grin.res = grin.results,
chrom = 9,
plot.start = 19900000,
plot.end = 25600000,
transTrack = FALSE,
show.ideogram = FALSE,
lesion.grp = "loss",
spec.lsn.clr = "blue"
)
# Plot all lesion types across a larger genomic region without transcript
# annotations.
lsn.transcripts.plot(
grin.res = grin.results,
chrom = 9,
plot.start = 1,
plot.end = 141000000,
transTrack = FALSE,
show.ideogram = FALSE,
point.size.mm = 1
)
## Not run:
# Transcript-track examples require an EnsDb annotation object retrieved
# through AnnotationHub and therefore require an internet connection.
ah <- AnnotationHub::AnnotationHub()
# Ensembl release 110 transcript annotations for human GRCh38.
hg38.transcripts <- ah[["AH113665"]]
# Define colors for the lesion types in the example dataset.
lesion.colors <- c(
fusion = "black",
gain = "red",
loss = "blue",
mutation = "olivedrab"
)
# Plot all transcripts and genomic lesions affecting JAK3.
lsn.transcripts.plot(
grin.res = grin.results,
gene = "JAK3",
transcript.mode = "all",
lsn.clrs = lesion.colors,
hg38.transcripts = hg38.transcripts,
hg38.cytoband = hg38_cytoband
)
# Display selected JAK1 transcripts and increase point-marker size.
lsn.transcripts.plot(
grin.res = grin.results,
gene = "JAK1",
transcript.mode = "selected",
selected.transcript = c(
"ENST00000342505",
"ENST00000672751"
),
lsn.clrs = lesion.colors,
point.size.mm = 0.7,
transcript.height = 0.40,
hg38.transcripts = hg38.transcripts,
hg38.cytoband = hg38_cytoband
)
# Plot transcript annotations and genomic lesions across a user-defined
# region while displaying gene names in the transcript track.
lsn.transcripts.plot(
grin.res = grin.results,
chrom = 9,
plot.start = 21900000,
plot.end = 21990000,
transcript.mode = "all",
show.transcript.labels = TRUE,
lsn.clrs = lesion.colors,
transcript.height = 0.46,
hg38.transcripts = hg38.transcripts,
hg38.cytoband = hg38_cytoband
)
## End(Not run)
GRIN2 documentation built on Aug. 22, 2026, 5:09 p.m.
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View source: R/lsn.transcripts.plot.R
| lsn.transcripts.plot | R Documentation |
Plot Genomic Lesions with Transcript Annotations
Description
Creates an integrated genomic-region plot combining patient-level genomic lesions with optional transcript annotations, chromosome context, genomic coordinates, lesion-type legends, and gene-level GRIN2 statistics.
The function supports both gene-centered plots and user-defined genomic regions. Single-position lesions, or lesion types explicitly selected by the user, are drawn at their exact genomic coordinates with user-controlled marker size.
Usage
lsn.transcripts.plot(
grin.res,
gene = NULL,
chrom = NULL,
plot.start = NULL,
plot.end = NULL,
transTrack = TRUE,
show.ideogram = TRUE,
show.axis = TRUE,
show.transcript.labels = FALSE,
transcript.mode = c("all", "selected"),
selected.transcript = NULL,
lesion.grp = NULL,
lsn.clrs = NULL,
spec.lsn.clr = NULL,
point.lesion.groups = NULL,
point.size.mm = 0.8,
expand = 0.0005,
hg38.transcripts = NULL,
hg38.cytoband = NULL,
genome = "hg38",
transcript.height = 0.31,
draw = TRUE
)
Arguments
grin.res |
A GRIN2 results object containing at least |
gene |
Optional character scalar specifying the gene to plot. When
supplied, genomic coordinates are obtained from |
chrom |
Chromosome for a user-defined regional plot. Used only when
|
plot.start, plot.end |
Numeric start and end coordinates for a
user-defined regional plot. Both are required when |
transTrack |
Logical; whether to display transcript annotations. |
show.ideogram |
Logical; whether to display a chromosome ideogram. |
show.axis |
Logical; whether to display a genomic-coordinate axis. |
show.transcript.labels |
Logical; whether transcript or gene labels are displayed within the transcript track. |
transcript.mode |
Character string specifying which transcript
annotations to display. Use |
selected.transcript |
Character vector of transcript IDs retained when
|
lesion.grp |
Optional character vector specifying lesion types to plot. |
lsn.clrs |
Optional named character vector assigning colors to lesion
types. Vector names must match the lesion-type values in
|
spec.lsn.clr |
Optional color used when a single lesion type is
selected through |
point.lesion.groups |
Optional character vector specifying lesion types
to display as point markers. When |
point.size.mm |
Positive numeric scalar specifying the diameter, in millimeters, of lesions displayed as circles. The default is 0.8. |
expand |
Non-negative numeric proportion used to expand a gene-centered plotting interval upstream and downstream. It is ignored for user-defined regional plots, which use the supplied coordinates exactly. |
hg38.transcripts |
An |
hg38.cytoband |
Cytoband annotation supplied to
|
genome |
Genome identifier passed to the Gviz annotation tracks. |
transcript.height |
Relative vertical space allocated to the transcript
annotation track. Increasing this value provides additional space when
many transcripts are displayed. This value is used only when
|
draw |
Logical; if |
Details
In gene mode, the displayed interval is derived from the matching entry in
gene.data and can be expanded using expand. In regional mode, the exact
interval specified by chrom, plot.start, and plot.end is used.
Transcript annotations can be shown in full or restricted to selected transcript IDs. Selected IDs are matched after removal of version suffixes. Unmatched IDs are reported in a warning when at least one requested transcript is available; the function stops with an informative error when none of the requested transcripts can be found.
Point-like lesions are plotted at their exact genomic start coordinates and use physical marker sizes measured in millimeters. Lesions are ordered first by lesion type and then by interval size, with source order used to break exact ties.
When transcript annotations are not displayed, the vertical space allocated to the ideogram and genomic-coordinate axis is reduced automatically so that the lesion panel occupies the available plotting area more efficiently.
For gene-centered plots, available lesion-specific subject counts and
transformed p- and q-values are displayed together with ordered
constellation statistics from gene.hits. Missing statistics are omitted
rather than preventing plot construction.
Value
Invisibly returns a gtable/grob object representing the assembled
figure. When draw = TRUE, the figure is also drawn.
See Also
grin.stats(), Gviz::GeneRegionTrack(),
Gviz::GenomeAxisTrack(), Gviz::IdeogramTrack(),
ensembldb::getGeneRegionTrackForGviz()
Examples
data("grin.results")
data("hg38_cytoband")
# Plot lesions across a user-defined genomic region without transcript
# annotations. This example uses only data included with GRIN2.
lsn.transcripts.plot(
grin.res = grin.results,
chrom = 9,
plot.start = 19900000,
plot.end = 25600000,
transTrack = FALSE,
show.ideogram = FALSE,
lesion.grp = "loss",
spec.lsn.clr = "blue"
)
# Plot all lesion types across a larger genomic region without transcript
# annotations.
lsn.transcripts.plot(
grin.res = grin.results,
chrom = 9,
plot.start = 1,
plot.end = 141000000,
transTrack = FALSE,
show.ideogram = FALSE,
point.size.mm = 1
)
## Not run:
# Transcript-track examples require an EnsDb annotation object retrieved
# through AnnotationHub and therefore require an internet connection.
ah <- AnnotationHub::AnnotationHub()
# Ensembl release 110 transcript annotations for human GRCh38.
hg38.transcripts <- ah[["AH113665"]]
# Define colors for the lesion types in the example dataset.
lesion.colors <- c(
fusion = "black",
gain = "red",
loss = "blue",
mutation = "olivedrab"
)
# Plot all transcripts and genomic lesions affecting JAK3.
lsn.transcripts.plot(
grin.res = grin.results,
gene = "JAK3",
transcript.mode = "all",
lsn.clrs = lesion.colors,
hg38.transcripts = hg38.transcripts,
hg38.cytoband = hg38_cytoband
)
# Display selected JAK1 transcripts and increase point-marker size.
lsn.transcripts.plot(
grin.res = grin.results,
gene = "JAK1",
transcript.mode = "selected",
selected.transcript = c(
"ENST00000342505",
"ENST00000672751"
),
lsn.clrs = lesion.colors,
point.size.mm = 0.7,
transcript.height = 0.40,
hg38.transcripts = hg38.transcripts,
hg38.cytoband = hg38_cytoband
)
# Plot transcript annotations and genomic lesions across a user-defined
# region while displaying gene names in the transcript track.
lsn.transcripts.plot(
grin.res = grin.results,
chrom = 9,
plot.start = 21900000,
plot.end = 21990000,
transcript.mode = "all",
show.transcript.labels = TRUE,
lsn.clrs = lesion.colors,
transcript.height = 0.46,
hg38.transcripts = hg38.transcripts,
hg38.cytoband = hg38_cytoband
)
## End(Not run)
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