# plotsr 0.5.4


{{< admonition tip "Conda" true >}}
See the 'activating the conda environment' section below to access this
software.
{{< /admonition >}}

## plotsr-0.5.4

Plotsr generates high-quality visualisation of synteny and structural
rearrangements between multiple genomes. For this, it uses the genomic
structural annotations between multiple chromosome-level assemblies.

See the [readme](https://github.com/schneebergerlab/plotsr) for examples and
to get example data.

### syri

[syri](https://github.com/schneebergerlab/syri) is included in the conda
environment so that the alignmetns can be done.

-------------------------------------------------------------------------------

## Activating the conda environment

Check out a node with `qrsh` and run:

```console
bash
source /local/cluster/conda-envs/envs/plotsr-0.5.4/activate.sh
```

And then run your commands as usual. To use over SGE, include the source line
above in a shell script prior to your commands, e.g.

```bash
$ cat run_plotsr.sh
#!/usr/bin/env bash
source /local/cluster/conda-envs/envs/plotsr-0.5.4/activate.sh
plotsr ...
```

And then run `SGE_Batch -c 'bash ./run_plotsr.sh' -r sge.plotsr ...`.

### Making activation easier

If you have had conda set up for a while, e.g. using the instructions in [this
post](../../tips/posts/using-the-system-miniconda-3-install/), then you can
run (only necessary once):

```console
bash
conda config --append envs_dirs /local/cluster/conda-envs/envs
conda config --append pkgs_dirs /local/cluster/conda-envs/pkgs
```

and then you can activate the env using `conda activate plotsr-0.5.4`.

## Location and version

```console
$ source /local/cluster/conda-envs/envs/plotsr-0.5.4/activate.sh
$ which plotsr
/local/cluster/conda-envs/envs/plotsr-0.5.4/bin/plotsr
$ plotsr --version
0.5.4
```

## help message

```console
$ plotsr --help
usage: Plotting structural rearrangements between genomes [-h] [--sr SR]
                                                          [--bp BP] --genomes
                                                          GENOMES
                                                          [--markers MARKERS]
                                                          [--tracks TRACKS]
                                                          [--chrord CHRORD]
                                                          [--chrname CHRNAME]
                                                          [-o O] [--itx]
                                                          [--chr CHR]
                                                          [--reg REG] [--rtr]
                                                          [--nosyn] [--noinv]
                                                          [--notr] [--nodup]
                                                          [-s S] [--cfg CFG]
                                                          [-R] [-f F] [-H H]
                                                          [-W W] [-S S] [-d D]
                                                          [-b {agg,cairo,pdf,pgf,ps,svg,template}]
                                                          [-v]
                                                          [--log {DEBUG,INFO,WARN}]
                                                          [--version]

Input/Output files:
  --sr SR               Structural annotation mappings (syri.out) identified by
                        SyRI (default: None)
  --bp BP               Structural annotation mappings in BEDPE format
                        (default: None)
  --genomes GENOMES     File containing path to genomes (default: None)
  --markers MARKERS     File containing path to markers (bed format) (default:
                        None)
  --tracks TRACKS       File listing paths and details for all tracks to be
                        plotted (default: None)
  --chrord CHRORD       File containing reference (first genome) chromosome IDs
                        in the order in which they are to be plotted. File
                        requires one chromosome ID per line. Not compatible
                        with --chr (default: None)
  --chrname CHRNAME     File containing reference (first genome) chromosome
                        names to be used in the plot. File needs to be a TSV
                        with the chromosome ID in first column and chromosome
                        name in the second. (default: None)
  -o O                  Output file name. Acceptable format: pdf, png, svg
                        (default: plotsr.pdf)

Data filtering:
  --itx                 Use inter-chromosomal plotting mode (experimental)
                        (default: False)
  --chr CHR             Select specific chromosome on reference (first genome)
                        and plots them in the given order. Not compatible with
                        --chrord. Can be used multiple time to select more than
                        one chromosomes. (default: None)
  --reg REG             Plots a specific region. Use as:
                        GenomeID:ChromosomeID:Start-End. Not compatible with
                        --chr and -R. (default: None)
  --rtr                 When using --reg, plot all SRs that are within the
                        boundaries of the homologous regions. For highly zoomed
                        regions, this could result in visually disconnected
                        alignments. (default: False)
  --nosyn               Do not plot syntenic regions (default: False)
  --noinv               Do not plot inversions (default: False)
  --notr                Do not plot translocations regions (default: False)
  --nodup               Do not plot duplications regions (default: False)
  -s S                  minimum size of a SR to be plotted (default: 10000)

Plot adjustment:
  --cfg CFG             Path to config file containing parameters to adjust
                        plot. (default: None)
  -R                    Join adjacent syntenic blocks if they are not
                        interrupted by SRs. Using this would decrease gaps in
                        the visualisation. (default: False)
  -f F                  font size (default: 6)
  -H H                  height of the plot (default: None)
  -W W                  width of the plot (default: None)
  -S S                  Space for homologous chromosome (0.1-0.75). Adjust this
                        to make more space for annotation markers/texts and
                        tracks. (default: 0.7)
  -d D                  DPI for the final image (default: 300)
  -b {agg,cairo,pdf,pgf,ps,svg,template}
                        Matplotlib backend to use (default: agg)
  -v                    Plot vertical chromosome (default: False)

optional arguments:
  -h, --help            show this help message and exit
  --log {DEBUG,INFO,WARN}
                        Log-level (default: WARN)
  --version             show program's version number and exit
```

software ref: <https://github.com/schneebergerlab/plotsr>  
software ref: <https://github.com/schneebergerlab/syri>  
research ref: <https://doi.org/10.1093/bioinformatics/btac196>