plot_regions_relative_to_reference: Generate segment plot to visualize genomic regions related to...

In cparsania/parcutils: Utility Functions To Deal Day To Day Bioinformatics Tasks.

Generate segment plot to visualize genomic regions related to reference regions.

Description

Generate segment plot to visualize genomic regions related to reference regions.

Usage

plot_regions_relative_to_reference(query, reference)

Arguments

query	an object of GenomicRanges::granges() to be visualized relative to reference
reference	an object of GenomicRanges::granges() against which query regions should be mapped.

Value

a list containing segment plot and plot data

Examples

## Not run: 
ref_file <- system.file("extdata", "Homo_sapiens.GRCh38.101.gtf.gz" ,package = "parcutils")
ref_data <- rtracklayer::import(ref_file)  %>%
 tibble::as_tibble() %>%
 dplyr::mutate(seqnames = stringr::str_c("chr",seqnames ,sep = "")) %>% plyranges::as_granges()
 ref_data_gr <-  ref_data %>%
dplyr::filter(type == "gene" & gene_biotype == "protein_coding")
query_regions_gr <- ref_data %>% dplyr::filter(type == "Selenocysteine")  %>% sample(5000)

oo <- plot_regions_relative_to_reference(query = query_regions_gr, reference  =  ref_data_gr)
 oo$plot
oo$data %>% ggplot2::ggplot(aes(x = q_relt_start)) + geom_density()

## End(Not run)

cparsania/parcutils documentation built on Oct. 27, 2024, 4:55 a.m.