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.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive [user@cn4338 ~]$ module load plotsr [+] Loading plotsr 1.1.0 on cn4326 [+] Loading singularity 3.10.5 on cn4326
Running help command:
[user@cn4338] cp -a /usr/local/apps/plotsr/1.1.0/example .
[user@cn4338 example]$ plotsr -h
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] [--lf LOGFIN]
[--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
--lf LOGFIN Name of log file (default: plotsr.log)
--log {DEBUG,INFO,WARN}
Log-level (default: WARN)
--version show program's version number and exit
Example Visualization
## Unzip gene annotation and SNPs file. These would be plotted as tracks. [user@cn4338] cp -a /usr/local/apps/plotsr/1.1.0/example . [user@cn4338] cd example/ [user@cn4338 example]$gzip -d TAIR10_GFF3_genes.gff.gz [user@cn4338 example]$ gzip -d 1001genomes.snps.sorted.bed.gz # Plot using plotsr [user@cn4338 example]$ plotsr \ --sr col_lersyri.filtered.out \ --sr ler_cvisyri.filtered.out \ --sr cvi_erisyri.filtered.out \ --genomes genomes.txt \ -o output_plot.png 2024-01-17 13:31:14,247 - Plotsr - INFO - Starting 2024-01-17 13:31:17,163 - Plotsr - INFO - Plot output_plot.png generated. 2024-01-17 13:31:17,163 - Plotsr - INFO - Finished
| For more examples, please visit the Plotsr Example Github Page |