+ By default the transcript isoform with the highest coverage is drawn. Alternatively, the transcript isoform that is provided in the columns @@ -81,14 +82,6 @@ - - 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 @@ -100,7 +93,24 @@ - + + 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 @@ -151,6 +161,67 @@ help="Default: 8.267"/> + + 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+)?$ +