Visualize exon-intron structure of transcripts on genomic scale.

  genes = NULL,
  one_to_one = NULL,
  tested_transcripts_only = "mixed",
  reduce_introns = TRUE,
  reduce_introns_fill = "white",
  reduce_introns_min_size = 50,
  include_ID_in_title = TRUE,
  fontsize_vec = c(10, 1.1, 0.6),
  arrow_colors = c("#7CAE00", "#00BFC4"),
  arrow_start = 0.88,
  extension_factors = c(0.025, 0.22),
  savepath = NULL,
  filename_ext = "_transcripts.png",
  add_to_table = FALSE,
  BPPARAM = BiocParallel::SerialParam(),



dturtle result object of posthoc_and_stager().


Character vector of genes to plot. If NULL, defaults to all found significant genes (sig_genes).


Either path to a gtf/gff file which will be read or a granges object of a already read in gtf/gff file. Such an object can be created with import_gtf("GTF_PATH", feature_type=NULL, out_df=FALSE). See import_gtf() for more information.


The genome on which to create the ideogram tracks. This has to be a valid UCSC genome identifier (e.g. 'hg38', 'mm10', 'danRer11', etc.). Can also be NULL to skip ideogram track generation.


Specify TRUE, if one_to_one mapping of gene/transcript identifiers with their respective names was enforced before (with one_to_one_mapping()). If a non default extension character (ext) has been used, please specify the used extension character.


Specify, if only transcripts which were tested in DTU analysis should be plotted. This are only the not-filtered transcripts of significant genes. Defaults to mixed, meaning if a gene has no tested transcripts (i.e. it was not significant), it defaults to all non-filtered transcripts of this gene. Can also be FALSE to allow all transcripts, or TRUE to exclude all untested transcripts.


Logical if intron ranges shall be shrunken down, highlighting the exonic structure.


Optionally specify the background color of ranges where introns have been reduced.


Specify the minimal size introns are reduced to (in bp).


Logial, if the Gene-ID should be included in the plot title. Defaults to TRUE.


Vector of fontsizes to use. The first value is the side annotation text fontsize (in pt), the second value the cex factor for the title, the third value the cex factor for the feature & chromosome names.


Specify the colors of the arrows indicating the direction of proportional changes. The first color string is for a positive change, the second for a negative one.


Advanced: Set the x coordinate of the arrow annotations (in NPC)


Advanced: Specify the extension factors to extend the plotted genomic range. The first value if for the extension of the front (left) side, the second for the back (right).


If you want your files to be saved to disk, specify a save path here. The directories will be created if necessary.


Optionally specify a file name extension here, which also defines the save image format. The file name will be 'gene_name+extension'.


If a savepath is provided, add the filepaths of the created plots to the corresponding entries in dtu_table. The name of the column that shall be created can be specified here.


If multicore processing should be used, specify a BiocParallelParam object here. Among others, can be SerialParam() (default) for non-multicore processing or MulticoreParam('number_cores') for multicore processing. See BiocParallel for more information.


Arguments passed down to png or cairo_pdf or pdf or jpeg, depending on filename_ext ending and capabilities (cairo_pdf or pdf).


Returns list of saved plots, for adding to the DTU table. If no savepath is provided, returns a list of the created plots for further processing.


Reduced intron length is computed by taking the square root, but is not less than the specified reduce_introns_min_size length. If less GRanges are found than expected, try setting one_to_one to TRUE or the used extension character. When calling this function many times, try importing the GTF-File with gtf <- import_gtf("GTF_PATH", feature_type=NULL, out_df=FALSE) once and pass it to the gtf parameter to improve performance.

See also

run_drimseq() and posthoc_and_stager() for DTU object creation. create_dtu_table() and plot_dtu_table() for table visualization.

Other DTUrtle visualization: create_dtu_table(), plot_dimensional_reduction(), plot_proportion_barplot(), plot_proportion_pheatmap()