GRIN2 (version 2.0.0)

grin.stats.lsn.plot: GRIN Statistics Lesions Plot

Description

Generates a plot showing all lesion types that span a specified gene or regulatory feature with GRIN stats added.

Usage

grin.stats.lsn.plot(grin.res, feature = NULL, lsn.clrs = NULL, expand = 5e-04)

Value

A two-panel plot showing lesion distribution and GRIN statistics for a given gene or regulatory feature, without a transcript annotation panel.

Arguments

grin.res

GRIN results for genes or regulatory elements, as returned by the grin.stats function.

feature

Ensembl ID of a feature of interest. This can be either a gene (e.g., Ensembl gene ID) or a regulatory region from Ensembl Regulatory Build or FANTOM5 project.

lsn.clrs

Named vector of colors for each lesion type. If not provided, colors are automatically assigned using default.grin.colors.

expand

Numeric value that controls the proportion of the flanking region (upstream/downstream) around the gene to be included. Default is 0.0005. Set to 0 to restrict the plot strictly to the locus boundaries.

Author

Abdelrahman Elsayed and Stanley Pounds

Details

The plot consists of two panels:

• Top panel: Displays all lesion types overlapping the selected gene or regulatory feature. Lesions are color-coded by type, as indicated in the legend.

• Bottom panel: Summarizes GRIN statistics for the feature, including the number of subjects affected per lesion type, and the corresponding \(-\log_{10}(p)\) and \(-\log_{10}(q)\) values for significance.

This plot is particularly useful for regulatory features, which typically lack transcript structure. Therefore, no transcript or exon structure is shown.

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)

# Run GRIN analysis
grin.results <- grin.stats(lesion_data,
                           hg38_gene_annotation,
                           hg38_chrom_size)

# Plot lesion and GRIN stats for a gene of interest (e.g., WT1)
grin.stats.lsn.plot(grin.results, feature = "ENSG00000184937")

# Can also be also used for regulatory features without transcript panels