| 40 | | * plot_shared_loci.R |
| 41 | | |
| 42 | | ** Plots the shared/unique loci in the two datasets per individual as a barplot ** Usage: Rscript plot_shared_loci.R <concordance_file> <out_plot.jpg> [name_dataset1] [name_dataset2] |
| 43 | | |
| 44 | | * plot_geno_concordance.R |
| 45 | | |
| 46 | | ** Plots the genotype concordance between two datasets per individual as a barplot ** Usage: Rscript plot_geno_concordance.R <concordance_file> <out_plot.jpg> [plot_title] |
| 47 | | |
| 48 | | * plot_discordance_matrix.R |
| 49 | | |
| 50 | | ** Plots the genotype discordance by "discordance type" (0/0 -> 0/1, 0/0 -> 1/1, 0/1 -> 0/0, etc.) ** Usage: Rscript plot_discordance_matrix.R <discordance_matrix_file> <out_plot.jpg> [dataset1_name] [dataset2_name] [show_concordant_data=FALSE] [<concordance_file>] ** Note: *** The last optional argument is a concordance file over the same data to plot as 'unknown' all loci that were not captured by the concordance matrix since the alleles were not exact matches (e.g. if one of the allele was monomorphic in one set). |
| 51 | | |
| | 39 | For reporting purpose, R scripts were created. These scripts all take files created using vcftools-diff_site-condordance.pl or vcftools-discordance-matrix.py as input. |
| | 40 | The following scripts are available: |
| | 41 | * plot_shared_loci.R |
| | 42 | ** Plots the shared/unique loci in the two datasets per individual as a barplot |
| | 43 | ** Usage: Rscript plot_shared_loci.R --in <concordance_file> --out <out_plot.jpg> [--data1 name_dataset1] [--data2 name_dataset2] |
| | 44 | * plot_geno_concordance.R |
| | 45 | ** Plots the genotype concordance between two datasets per individual as a barplot |
| | 46 | ** Usage: Rscript plot_geno_concordance.R --in <concordance_file> --out <out_plot.jpg> [--title plot_title] |
| | 47 | * plot_discordance_matrix.R |
| | 48 | ** Plots the genotype discordance by "discordance type" (0/0 -> 0/1, 0/0 -> 1/1, 0/1 -> 0/0, etc.) |
| | 49 | ** Usage: Rscript plot_discordance_matrix.R --in <discordance_matrix_file> --out <out_plot.jpg> [--data1 dataset1_name] [--data2 dataset2_name] [--show_concordant] [--show unknowns <concordance_file>] |
