Visualize transcripts on genomic scale

Visualize exon-intron structure of transcripts on genomic scale.

plot_transcripts_view(
  dturtle,
  genes = NULL,
  gtf,
  genome,
  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(),
  ...
)

Arguments

dturtle	`dturtle` result object of `posthoc_and_stager()`.
genes	Character vector of genes to plot. If `NULL`, defaults to all found significant genes (`sig_genes`).
gtf	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.
genome	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.
one_to_one	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.
tested_transcripts_only	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.
reduce_introns	Logical if intron ranges shall be shrunken down, highlighting the exonic structure.
reduce_introns_fill	Optionally specify the background color of ranges where introns have been reduced.
reduce_introns_min_size	Specify the minimal size introns are reduced to (in bp).
include_ID_in_title	Logial, if the Gene-ID should be included in the plot title. Defaults to TRUE.
fontsize_vec	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.
arrow_colors	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.
arrow_start	Advanced: Set the x coordinate of the arrow annotations (in NPC)
extension_factors	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).
savepath	If you want your files to be saved to disk, specify a save path here. The directories will be created if necessary.
filename_ext	Optionally specify a file name extension here, which also defines the save image format. The file name will be 'gene_name+extension'.
add_to_table	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.
BPPARAM	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).

Value

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.

Details

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.

Arguments

Value

Details

See also