Allow region_coords in plotCoverage while rescale_introns = TRUE
whtns opened this issue · comments
This is a great package. I'm using in a shiny app. I'd like to plot a specific sub-genomic region while rescaling introns. I could do this with ggplot xlim (I think) but I'd also like to extract the coverage data and return to the user.
# set up code
require("dplyr")
require("GenomicRanges")
sample_data = dplyr::data_frame(sample_id = c("aipt_A", "aipt_C", "bima_A", "bima_C"),
condition = factor(c("Naive", "LPS", "Naive", "LPS"), levels = c("Naive", "LPS")),
scaling_factor = 1) %>%
dplyr::mutate(bigWig = system.file("extdata", paste0(sample_id, ".str2.bw"), package = "wiggleplotr"))
track_data = dplyr::mutate(sample_data, track_id = condition, colour_group = condition)
selected_transcripts = c("ENST00000438495", "ENST00000392477") #Plot only two transcripts of the gens
# This works
plotCoverage(ncoa7_exons[selected_transcripts], ncoa7_cdss[selected_transcripts],
ncoa7_metadata, track_data,
heights = c(2,1), fill_palette = getGenotypePalette(),
rescale_introns = FALSE,
region_coords = c(125900000, 125950000)
)
# This does not work
plotCoverage(ncoa7_exons[selected_transcripts], ncoa7_cdss[selected_transcripts],
ncoa7_metadata, track_data,
heights = c(2,1), fill_palette = getGenotypePalette(),
# rescale_introns = FALSE,
region_coords = c(2000, 4000)
)