kauralasoo / wiggleplotr Goto Github PK
View Code? Open in Web Editor NEWA small R package to make sequencing read coverage plots in R.
License: Apache License 2.0
A small R package to make sequencing read coverage plots in R.
License: Apache License 2.0
Hi Kaur,
Hope you are well. Your tool has been very useful for me lately to visualize transcript isoforms.
My input object is typically a Granges object imported from a custom-assembled GTF. It would be nice to have a function to plotTranscriptsFromGTF function that conveniently group the exon and cds features by transcript and plot it out. Users may specify which gene/transcript to plot by providing an argument to filter the GTF by a logical expression (eg gene_name == "Ncoa7"). Unfiltered GTF may not be plotted as transcripts have different seqlevels.
What do you think of this feature? I do have an idea on how to implement it and would like to create a pull request if you think this idea is feasible.
Fursham
Hi,
sorry for the (too) late heads up! I've removed the filter classes from ensembldb
, so your package is currently failing on Bioc!
I'll forking the package, fixing it and make a pull request.
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)
)
Hi,
If I am interested in plotting "ncRNA" how can I remove or change the cdss
of the function?
Thanks!
Hi, im using wiggleplotr to plot transcripts and it works very nicely for me.
I was wondering if there would be a possibility to add exon labeling to the plot, i.e. numbering of the exons. Such that when comparing different isoforms of one gene one could immediately see which exon is missing in one isoform for example.
Hi,
I am not able to execute this function due to this error.
Any ideas what could be the issue?
Error in seqinfo(con) : UCSC library operation failed
In addition: Warning message:
In seqinfo(con) :Couldn't open /Bigdata/Dropbox (Technion Dropbox)/Rina_Benel/Home/Rina/AS_linc/cardiac_diff/data/ChIPData/TrialCovData/EXP053380.bw
Can we implement scales = "free_y" for the read coverage plots?
Hello,
I am only interested in the output of plotTranscripts
. Is there a way to control the order of the transcripts plotted?
Hi,
Great package!
Possible to add function for log2 transformation in plotCoverage? Such a feature is possible in e.g. IGV.
Best,
Peter
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