- - By default the transcript isoform with the highest coverage is drawn. - Alternatively, the transcript isoform that is provided in the columns - transcript_id1 and transcript_id2 in the given fusions file can be drawn. - Selecting the isoform with the highest coverage usually produces nicer plots, - in the sense that the coverage track is smooth and shows a visible increase in coverage after the fusion breakpoint. - However, the isoform with the highest coverage may not be the one that is involved in the fusion. - Often, genomic rearrangements lead to non-canonical isoforms being transcribed. - For this reason, it can make sense to rely on the transcript selection provided by the columns transcript_id1/2, - which reflect the actual isoforms involved in a fusion. -\ As a third option, the transcripts that are annotated as canonical can be drawn. - Transcript isoforms tagged with appris_principal, appris_candidate, or CCDS are considered canonical. - - - - - - - The fusion of interest is drawn as a solid line in the circos plot. - To give an impression of the overall degree of rearrangement, - all other fusions are drawn as semi-transparent lines in the background. - This option determines which other fusions should be included in the circos plot. - Values specify the minimum confidence a fusion must have to be included. - It usually makes no sense to include low-confidence fusions in circos plots, - because they are abundant and unreliable, and would clutter up the circos plot. - Default: medium - - - - - - - - This option only applies to intergenic breakpoints. - If it is set to a value greater than 0, then the script draws the genes - which are no more than the given distance away from an intergenic breakpoint. - Note that this option is incompatible with squishIntrons. - Default: 0 - - - - Exons usually make up only a small fraction of a gene. - They may be hard to see in the plot. i - Since introns are in most situations of no interest in the context of gene fusions, - this switch can be used to shrink the size of introns to a fixed, negligible size. - It makes sense to disable this feature, if breakpoints in introns are of importance. - Default: TRUE - - - - - - - Occasionally, domains are annotated redundantly. - For example, tyrosine kinase domains are frequently annotated as - Protein tyrosine kinase and Protein kinase domain. - In order to simplify the visualization, such domains can be merged into one, - given that they overlap by the given fraction. - The description of the larger domain is used. - Default: 0.9 - - - - By default the number of an exon is printed inside each exon, - which is taken from the attribute exon_number of the GTF annotation. - When a gene has many exons, the boxes may be too narrow to contain the labels, - resulting in unreadable exon labels. In these situations, i - it may be better to turn off exon labels. - Default: TRUE - - - - - - Whether light and shadow should be rendered to give objects a 3D effect. - Default: TRUE - - - - - - By default, the script colorizes domains according to the colors - specified in the file given in --annotation. - This way, coloring of domains is consistent across all proteins. - But since there are more distinct domains than colors, - this can lead to different domains having the same color. - If this option is set to TRUE, the colors are recomputed for each fusion separately. - This ensures that the colors have the maximum distance for each individual fusion, - but they are no longer consistent across different fusions. - Default: FALSE - - - - - - - - - -