├── .gitignore ├── .project ├── .travis.yml ├── LICENSE.txt ├── README.md ├── docs ├── file_formats.textile ├── introduction.textile ├── null_rsq_phys_color.png ├── snapshot_tool.png └── usage.textile ├── html ├── null_rsq_phys_color.png ├── snapshot_tool.png ├── snp.css ├── snp.plotter.html ├── sp.png └── up_arrow.png ├── releases ├── snp.plotter_0.2.tar.gz ├── snp.plotter_0.3.1.tar.gz ├── snp.plotter_0.3.tar.gz ├── snp.plotter_0.4.tar.gz ├── snp.plotter_0.5.1.tar.gz └── snp.plotter_0.5.tar.gz ├── snp.plotter.20SNP.dataset.zip ├── snp.plotter.20SNP.dataset ├── config.txt ├── d1_hap.txt ├── d1_ss.txt ├── d2_hap.txt ├── d2_ss.txt ├── null_d1_controls.dat ├── null_rsq_phys_color.eps ├── null_rsq_phys_color.pdf └── palette.txt ├── snp.plotter ├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R │ └── snp.plotter.R ├── inst │ ├── CITATION │ ├── ChangeLog │ ├── NEWS │ └── extdata │ │ ├── config.txt │ │ ├── config_eps_lines_35.txt │ │ ├── config_pdf_lines_7.txt │ │ ├── config_pdf_lines_7_marker_lines.txt │ │ ├── config_pdf_no_lines_35.txt │ │ ├── d1_hap.txt │ │ ├── d1_ss.txt │ │ ├── d2_hap.txt │ │ ├── d2_ss.txt │ │ ├── null_d1_controls.dat │ │ ├── null_rsq_phys_color_eps_lines_35.eps │ │ ├── null_rsq_phys_color_original.pdf │ │ ├── null_rsq_phys_color_pdf_lines_7.pdf │ │ ├── null_rsq_phys_color_pdf_lines_7_marker_lines.pdf │ │ ├── null_rsq_phys_color_pdf_no_lines_35.pdf │ │ └── palette.txt ├── man │ ├── create.color.list.Rd │ ├── create.symbol.list.Rd │ ├── draw.legend.Rd │ ├── draw.plot.grid.hap.Rd │ ├── draw.plot.grid.setup.Rd │ ├── draw.plot.grid.snp.names.Rd │ ├── draw.plot.grid.ss.Rd │ ├── draw.plot.ld.plot.Rd │ ├── fix.values.Rd │ ├── read.config.Rd │ ├── retrieve.data.Rd │ ├── set.image.parameters.Rd │ └── snp.plotter.Rd ├── snp.plotter.Rproj └── vignettes │ ├── docs │ └── null_rsq_phys_color.png │ └── using_snp_plotter.Rmd └── src └── snp_plotter.Rpad /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | -------------------------------------------------------------------------------- /.project: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/.project -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/.travis.yml -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/README.md -------------------------------------------------------------------------------- /docs/file_formats.textile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/docs/file_formats.textile -------------------------------------------------------------------------------- /docs/introduction.textile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/docs/introduction.textile -------------------------------------------------------------------------------- /docs/null_rsq_phys_color.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/docs/null_rsq_phys_color.png -------------------------------------------------------------------------------- /docs/snapshot_tool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/docs/snapshot_tool.png -------------------------------------------------------------------------------- /docs/usage.textile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/docs/usage.textile -------------------------------------------------------------------------------- /html/null_rsq_phys_color.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/html/null_rsq_phys_color.png -------------------------------------------------------------------------------- /html/snapshot_tool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/html/snapshot_tool.png -------------------------------------------------------------------------------- /html/snp.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/html/snp.css -------------------------------------------------------------------------------- /html/snp.plotter.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/html/snp.plotter.html -------------------------------------------------------------------------------- /html/sp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/html/sp.png -------------------------------------------------------------------------------- /html/up_arrow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/html/up_arrow.png -------------------------------------------------------------------------------- /releases/snp.plotter_0.2.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/releases/snp.plotter_0.2.tar.gz -------------------------------------------------------------------------------- /releases/snp.plotter_0.3.1.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/releases/snp.plotter_0.3.1.tar.gz -------------------------------------------------------------------------------- /releases/snp.plotter_0.3.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/releases/snp.plotter_0.3.tar.gz -------------------------------------------------------------------------------- /releases/snp.plotter_0.4.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/releases/snp.plotter_0.4.tar.gz -------------------------------------------------------------------------------- /releases/snp.plotter_0.5.1.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/releases/snp.plotter_0.5.1.tar.gz -------------------------------------------------------------------------------- /releases/snp.plotter_0.5.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/releases/snp.plotter_0.5.tar.gz -------------------------------------------------------------------------------- /snp.plotter.20SNP.dataset.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter.20SNP.dataset.zip -------------------------------------------------------------------------------- /snp.plotter.20SNP.dataset/config.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter.20SNP.dataset/config.txt -------------------------------------------------------------------------------- /snp.plotter.20SNP.dataset/d1_hap.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter.20SNP.dataset/d1_hap.txt -------------------------------------------------------------------------------- /snp.plotter.20SNP.dataset/d1_ss.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter.20SNP.dataset/d1_ss.txt -------------------------------------------------------------------------------- /snp.plotter.20SNP.dataset/d2_hap.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter.20SNP.dataset/d2_hap.txt -------------------------------------------------------------------------------- /snp.plotter.20SNP.dataset/d2_ss.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter.20SNP.dataset/d2_ss.txt -------------------------------------------------------------------------------- /snp.plotter.20SNP.dataset/null_d1_controls.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter.20SNP.dataset/null_d1_controls.dat -------------------------------------------------------------------------------- /snp.plotter.20SNP.dataset/null_rsq_phys_color.eps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter.20SNP.dataset/null_rsq_phys_color.eps -------------------------------------------------------------------------------- /snp.plotter.20SNP.dataset/null_rsq_phys_color.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter.20SNP.dataset/null_rsq_phys_color.pdf -------------------------------------------------------------------------------- /snp.plotter.20SNP.dataset/palette.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter.20SNP.dataset/palette.txt -------------------------------------------------------------------------------- /snp.plotter/.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/.Rbuildignore -------------------------------------------------------------------------------- /snp.plotter/.gitignore: -------------------------------------------------------------------------------- 1 | /doc/ 2 | /Meta/ 3 | -------------------------------------------------------------------------------- /snp.plotter/DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/DESCRIPTION -------------------------------------------------------------------------------- /snp.plotter/NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/NAMESPACE -------------------------------------------------------------------------------- /snp.plotter/R/snp.plotter.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/R/snp.plotter.R -------------------------------------------------------------------------------- /snp.plotter/inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/CITATION -------------------------------------------------------------------------------- /snp.plotter/inst/ChangeLog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/ChangeLog -------------------------------------------------------------------------------- /snp.plotter/inst/NEWS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/NEWS -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/config.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/config.txt -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/config_eps_lines_35.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/config_eps_lines_35.txt -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/config_pdf_lines_7.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/config_pdf_lines_7.txt -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/config_pdf_lines_7_marker_lines.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/config_pdf_lines_7_marker_lines.txt -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/config_pdf_no_lines_35.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/config_pdf_no_lines_35.txt -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/d1_hap.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/d1_hap.txt -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/d1_ss.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/d1_ss.txt -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/d2_hap.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/d2_hap.txt -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/d2_ss.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/d2_ss.txt -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/null_d1_controls.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/null_d1_controls.dat -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/null_rsq_phys_color_eps_lines_35.eps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/null_rsq_phys_color_eps_lines_35.eps -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/null_rsq_phys_color_original.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/null_rsq_phys_color_original.pdf -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/null_rsq_phys_color_pdf_lines_7.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/null_rsq_phys_color_pdf_lines_7.pdf -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/null_rsq_phys_color_pdf_lines_7_marker_lines.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/null_rsq_phys_color_pdf_lines_7_marker_lines.pdf -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/null_rsq_phys_color_pdf_no_lines_35.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/null_rsq_phys_color_pdf_no_lines_35.pdf -------------------------------------------------------------------------------- /snp.plotter/inst/extdata/palette.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/inst/extdata/palette.txt -------------------------------------------------------------------------------- /snp.plotter/man/create.color.list.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/man/create.color.list.Rd -------------------------------------------------------------------------------- /snp.plotter/man/create.symbol.list.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/man/create.symbol.list.Rd -------------------------------------------------------------------------------- /snp.plotter/man/draw.legend.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/man/draw.legend.Rd -------------------------------------------------------------------------------- /snp.plotter/man/draw.plot.grid.hap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/man/draw.plot.grid.hap.Rd -------------------------------------------------------------------------------- /snp.plotter/man/draw.plot.grid.setup.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/man/draw.plot.grid.setup.Rd -------------------------------------------------------------------------------- /snp.plotter/man/draw.plot.grid.snp.names.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/man/draw.plot.grid.snp.names.Rd -------------------------------------------------------------------------------- /snp.plotter/man/draw.plot.grid.ss.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/man/draw.plot.grid.ss.Rd -------------------------------------------------------------------------------- /snp.plotter/man/draw.plot.ld.plot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/man/draw.plot.ld.plot.Rd -------------------------------------------------------------------------------- /snp.plotter/man/fix.values.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/man/fix.values.Rd -------------------------------------------------------------------------------- /snp.plotter/man/read.config.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/man/read.config.Rd -------------------------------------------------------------------------------- /snp.plotter/man/retrieve.data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/man/retrieve.data.Rd -------------------------------------------------------------------------------- /snp.plotter/man/set.image.parameters.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/man/set.image.parameters.Rd -------------------------------------------------------------------------------- /snp.plotter/man/snp.plotter.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/man/snp.plotter.Rd -------------------------------------------------------------------------------- /snp.plotter/snp.plotter.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/snp.plotter.Rproj -------------------------------------------------------------------------------- /snp.plotter/vignettes/docs/null_rsq_phys_color.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/vignettes/docs/null_rsq_phys_color.png -------------------------------------------------------------------------------- /snp.plotter/vignettes/using_snp_plotter.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/snp.plotter/vignettes/using_snp_plotter.Rmd -------------------------------------------------------------------------------- /src/snp_plotter.Rpad: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cannin/snp_plotter/HEAD/src/snp_plotter.Rpad --------------------------------------------------------------------------------