Generate a genomic context plot for a specified gene, displaying its transcripts
along with their types and annotations.
The function utilizes the plotgardener package to create a detailed
visualization of the genomic context, including an ideogram, chromosome
highlight, and transcript structures.
It requires a ContextData object that contains the necessary genomic
information and annotations.
The plot can be customized with various parameters such as offsets,
label limits, and ideogram references.
Usage
plot_genomic_context(
gene_name,
context_data,
limit_label = TRUE,
show_guides = FALSE,
y_offset = 0,
height_offset = 0,
downstream_offset = 0,
upstream_offset = 0,
ideogram_reference = c("hg38", "hg19", "mm11", "mm10", "none")
)Arguments
- gene_name
Character string specifying the name of the gene to plot.
- context_data
A
ContextDataobject containing genomic context information.- limit_label
Logical indicating whether to limit the length of transcript labels to avoid overlap (default is
TRUE).- show_guides
Logical indicating whether to show guide lines on the plot (default is
FALSE).- y_offset
Numeric value to adjust the vertical position of the plot (default is
0).- height_offset
Numeric value to adjust the height of the plot (default is
0).- downstream_offset
Numeric value to extend the downstream region beyond the gene's end position (default is
0).- upstream_offset
Numeric value to extend the upstream region beyond the gene's start position (default is
0).- ideogram_reference
Character string specifying the reference genome for the ideogram. Options include "hg38", "hg19", "mm11", "mm10", or "none" (default is "hg38").