#' @param 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.
#' @param 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.
#' @param 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.
#' @param 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.
#' @param reduce_introns Logical if intron ranges shall be shrunken down, highlighting the exonic structure.
#' @param reduce_introns_fill Optionally specify the background color of ranges where introns have been reduced.
#' @param reduce_introns_min_size Specify the minimal size introns are reduced to (in bp).
assertthat::assert_that(is.null(genes)||(methods::is(genes,"character")&&length(genes)>0),msg="The genes object must be a non-empty character vector or NULL.")
assertthat::assert_that(!missing(genome),msg="Please specify a UCSC genome identifier in `genome` (e.g. 'hg38', 'mm10', 'danRer11', etc.). Can also be NULL to skip ideogram track generation.")
assertthat::assert_that(is.null(genome)||methods::is(genome,"character")&&length(genome)==1,msg="The genome object must be a character vector of length 1 or NULL.")
assertthat::assert_that(is.null(one_to_one)||isTRUE(one_to_one)||(methods::is(one_to_one,"character")&&length(one_to_one)==1),msg="The one_to_one object must be a character vector of length 1, TRUE or NULL.")
assertthat::assert_that(length(tested_transcripts_only)==1&&tested_transcripts_only%in%c("mixed",T,F),msg="The tested_transcripts_only object must be 'mixed', TRUE or FALSE.")
assertthat::assert_that(is.logical(reduce_introns),msg="The reduce_introns objects must be logical.")
assertthat::assert_that(methods::is(reduce_introns_fill,"character")&&length(reduce_introns_fill)==1,msg="The reduce_introns_fill objects must be a character vector of length 1")
assertthat::assert_that((is.integer(reduce_introns_min_size)||(is.numeric(reduce_introns_min_size)&&all(reduce_introns_min_size==trunc(reduce_introns_min_size))))&&reduce_introns_min_size>=0,msg="The provided reduce_introns_min_size must be a positive integer.")
message("\nFound gtf GRanges for ",length(valid_genes)," of ",length(genes)," provided genes.")
if(length(valid_genes)<length(genes)){
message("\n\tIf you ensured one_to_one mapping of the transcript and/or gene id in the former DTU analysis, try to set 'one_to_one' to TRUE or the used extension character.")
