plotReadsRepartitionAnnotations(alignedData, gff_names_vec, expName, pdfFileName, genomeReferenceFile)- The first page contains 4 barplots giving respectively the number of each annotation by chromosomes (seqnames) (the correspondence between colors and annotations is given at the bottom), the number of annotations contained in each file of gff_names_vec argument, the number of reads that aligned to each chromosome and the length of each chromosome.
- The second page contains two pie charts: The first one gives the percentage of coverage of the reference genome by each annotation, correspondence of colors is given at the right of the pie chart. The second pie chart gives the percentage of reads that aligned to a particular annotation, correspondence of colors is also given at the right of the pie chart.
- The third page is another representation of the pie chart enabling to compare directly the difference of occupancy of each annotation with the number of reads aligned to it.
The 'genomeReferenceFile' is the path to a file containing information about the genome that has been used to align the reads. It is a 3 lines text files.
The same files are used for multiread (see vignette).
Some files are provided in the package for some of the most commonly used genomes. For a list of them type:
dir(pattern="*.ref", path=system.file("resources", package="Pasha"))
First line describes the number of chromosomes in the genomes. Second line contains the size (in bp) of all chromosomes (space separated). Last lines containes the names of the chromosomes (space separated).
Example : 3 43255 10345 2456 chrI chrII chrIII