kauralasoo / wiggleplotr Goto Github PK

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,
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

Hi,
If I am interested in plotting "ncRNA" how can I remove or change the cdss of the function?

Thanks!

Hello,

I am only interested in the output of plotTranscripts. Is there a way to control the order of the transcripts plotted?

Currently the upper bound of coveragePlot is usually overflowed with the signal (maximum point of coverage value) as shown in the plot screenshot above.

Can be better if Y-axis maximum is a little bit higher than max value of covPlot

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 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

https://github.com/38/d4-format

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.

Can we implement scales = "free_y" for the read coverage plots?

Hi,

Great package!
Possible to add function for log2 transformation in plotCoverage? Such a feature is possible in e.g. IGV.

Best,
Peter