+ + + 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 + + + + + + + + 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 + + + + + + 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. + The keywords closestGene and closestProteinCodingGene instruct the script + to dynamically determine the distance to the next (protein-coding) gene for each breakpoint. + Alternatively, instead of specifying a single distance + that is applied upstream and downstream of both breakpoints alike, + more fine-grained control over the region to be shown is possible by specifying four comma-separated values. + The first two values determine the region to the left and to the right of breakpoint 1; + the third and fourth values determine the region to the left and to the right of breakpoint 2. + Note that this option is incompatible with squishIntrons. + Default: 0 + + + + ^(closestGene|closestProteinCodingGene|\d+|\d+,\d+,\d+,\d+)$ + + + 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 + + + + + + + + + + + Default: Helvetica + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + By default, transcripts are scaled automatically to fill the entire page. + This parameter enforces a fixed scale to be applied to all fusions, + which is useful when a collection of fusions should be visualized and the sizes of all transcripts should be comparable. + A common use case is the visualization of a gene that is found to be fused to multiple partners. + By forcing all fusion plots to use the same scale, the fusions can be summarized as a collage + in a single plot one above the other with matching scales. + Note: The scale must be bigger than the sum of the biggest pair of transcripts to be drawn, + or else dynamic scaling is applied, because display errors would occur otherwise. + The default value is 0, which means that no fixed scale should be used + and that the scale should be adapted dynamically for each fusion. Default: 0 + + + + When the parameter --alignments is used, coverage plots are drawn above the transcripts of the fused genes. + The plots can be cropped at a fixed level by passing a non-zero value to this parameter. + When only a single value is given, both coverage plots (for gene1 and gene2) are cropped at the same level. + When two comma-separated values are given, the cutoffs can be specified independently for the two plots. + A value of 0 indicates that no cropping should be applied (i.e., the cutoff is set to the peak coverage) + and that the coverage plots of both genes should be on the same scale. This is the default behavior. + A value of 0,0 also indicates that no cropping should be applied, + but the coverage plots of the two genes have different scales: + each one is scaled individually to the peak coverage of the respective gene. + Default: 0 + + ^\d+(,\d+)?$ + +