Examples ======== Below are some examples of the kinds of transcript that ExonViz can create. SDHD ---- Visualise two variants in the SDHD gene .. code-block:: console exonviz --transcript "NM_003002.4:r.[274g>u;300del]" --exonnumber > SDHD.svg .. image:: ../figures/SDHD.svg NF1 --- Visualise NF1, setting the width of the figure to the size of the largest exon .. code-block:: console exonviz --transcript "ENST00000358273.9" --noncoding --width 3600 --height 75 > NF1-202.svg .. image:: ../figures/NF1-202.svg Schematic representation of DMD ------------------------------- Create a schematic visualisation of the DMD gene. Since this gene is very large, we will first export the exons to TSV format, and then modify each exon to have the same size. .. code-block:: bash # Write the exons in TSV format to dmd.tsv exonviz --transcript DMD --exonnumber --dump-exons DMD-schematic.tsv # Next, modify each exon to be 30 bp in your favorite text editor # Don't forget to also update the size of the coding region for each exon # (see the table below) # Finally, draw the exons from the TSV file exonviz --exon-tsv DMD-schematic.tsv --width 750 --gap 0 > DMD-schematic.svg .. image:: ../figures/DMD-schematic.svg .. csv-table:: TSV file for schematic representation of DMD :delim: tab :file: ../figures/DMD-schematic.tsv DM20 and PLP1 -------------- The PLP1 gene has two main isoforms, namely `PLP1 (ENST00000621218.5)` and `DM20 (ENST00000619236.1)`. `DM20` is the shorter form of the protein, missing the last 35 amino acids from the third exon. Either isoform can be drawn by ExonViz directly. In the literature, the third exon is often divided in two parts. The first part, termed `3A` is present in each isoform, while the second part, termed `3B`, is missing from `DM20` (for example, `Shy et al., 2016 `_). The figure and associated TSV file are shown below, note that exon 3 has been split into two parts, `3A` and `3B`. .. code-block:: bash exonviz --exon-tsv PLP1-DM20.tsv --scale 1.3 --gap 0 > PLP1-DM20.svg .. image:: ../figures/PLP1-DM20.svg .. csv-table:: TSV file for PLP1 and DM20 :delim: tab :file: ../figures/PLP1-DM20.tsv NDUFAF6 cryptic exon -------------------- `Catania et al., 2018 `_ describe a deep intronic variant in `NDUFAF6` which leads to the inclusion of a 124nt cryptic exon. .. code-block:: bash exonviz --exon-tsv NDUFAF6.tsv > NDUFAF6.svg .. image:: ../figures/NDUFAF6.svg .. csv-table:: TSV file for NDUFAF6 cryptic exon :delim: tab :file: ../figures/NDUFAF6.tsv CYLD ---- `CYLD` is a tumor suppressor gene, which has a clear mutational hotspot in exon 16. In the figure below, all `ClinVar `_ variants for CYLD transcript `NM_001378743.1` have been visualized using ExonViz. This figure uses colors that are clearly distinguishable for color blind people, thanks to `this useful website `_. .. image:: ../figures/CYLD.svg How to create the figure ^^^^^^^^^^^^^^^^^^^^^^^^ Generating a figure such as this is fairly involved, since it requires gathering all variants for a given transcript, and then modifying them so they are displayed per category. Gather the variants ^^^^^^^^^^^^^^^^^^^ The following should be repeated for every variant category of interest, we will use the category `Likely Pathogenic` as an example. At the time of writing, this gives the following HGVS description: `NM_001378743.1(CYLD):c.[454_455del;1111del;2040dup;2282_2283del;2616del;2723dup]`. Note that intronic variants such as `1684+2T>C` should not be included, since they are outside of the exons. #. Visit `ClinVar `_ and Download all variants in Tabular (text) format. #. Open the file in a spreadsheet program, and order all variants using the `Germline consequence` option. #. Create a compound HGVS description for all variants in a category, for example `Likely Pathogenic`. Export the variants ^^^^^^^^^^^^^^^^^^^ Use ExonViz to export the exons and variants to TSV files to maninpulate .. code-block:: bash exonviz --dump-variants likely-pathogenic.tsv --transcript "NM_001378743.1:c.[454_455del;1111del;2040dup;2282_2283del;2616del;2723dup]" --scale 1.2 > /dev/null .. csv-table:: Raw likely pathogenic variants for CYLD :delim: tab :file: ../figures/CYLD-example.tsv Update the variants ^^^^^^^^^^^^^^^^^^^ Open the `likely-pathogenic.tsv` file in a spreadsheet program, and update the **name** column to contain `(Likely) Pathognic`, and the **color** option to `#882255` for each variant. .. csv-table:: Updated likely pathogenic variants for CYLD :delim: tab :file: ../figures/CYLD-example-update.tsv Draw the figure with ExonViz ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Repeat the above steps for each category from ClinVar you are interested in. When you are satisfied with the variants, you can merge all categories into a single file. You can then draw CYLD from the tsv files you have created. ExonViz will recognise that there are multiple variants with the same `name` and `color`, and will only include each combination in the legend only once. .. code-block:: bash exonviz --width 747 --exon-tsv CYLD-exons.tsv --variant-tsv CYLD-variants.tsv --scale 1.2 --variantshape bar > CYLD.svg .. csv-table:: Exons for CYLD :delim: tab :file: ../figures/CYLD-exons.tsv .. csv-table:: Variants for CYLD :delim: tab :file: ../figures/CYLD-variants.tsv