In this section we show how to plot different graphics with the function plot. A complete description can be viewed with ?plot.fullsib_scan.

As an example we will use the data that comes with with the package. First, the steps below are needed; they were described in the fullsibQTL Tutorial vignette.

After, to plot a basic graphic:

Customization

The codes below are self-explained. There are a number of modifications in the graphics that can be easily implemented.

You can check more colors options at this cheatsheet or at this color guide

You can also customize the plot with the default R plot.default options, such as main, ylab, xlab, yaxt, ylim, etc.

Adding QTL locations

The mapped QTLs are the same explained on the fullsibQTL Tutorial vignette:

The usage of function plot to add QTL is not so straightforward as to the one of plot_fullsibQTL. It is necessary to use function points as follows. Knowing that the gap space is 50, we can add this to the total size of each LG and get the position. The points will be localized at:

And then:

Session Info

sessionInfo()
#> R version 3.6.3 (2020-02-29)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 19.10
#> 
#> Matrix products: default
#> BLAS:   /usr/local/lib/R/lib/libRblas.so
#> LAPACK: /usr/local/lib/R/lib/libRlapack.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] fullsibQTL_0.0.9007 onemap_2.1.3        rmdformats_0.3.7   
#> [4] knitr_1.28         
#> 
#> loaded via a namespace (and not attached):
#>   [1] colorspace_1.4-1        ellipsis_0.3.1          class_7.3-15           
#>   [4] rio_0.5.16              htmlTable_1.13.3        base64enc_0.1-3        
#>   [7] rstudioapi_0.11         mice_3.9.0              codetools_0.2-16       
#>  [10] splines_3.6.3           doParallel_1.0.15       Formula_1.2-3          
#>  [13] polynom_1.4-0           jsonlite_1.6.1          MDSMap_1.1             
#>  [16] broom_0.5.6             cluster_2.1.0           png_0.1-7              
#>  [19] shiny_1.4.0.2           httr_1.4.1              compiler_3.6.3         
#>  [22] backports_1.1.7         lazyeval_0.2.2          assertthat_0.2.1       
#>  [25] Matrix_1.2-18           fastmap_1.0.1           later_1.0.0            
#>  [28] acepack_1.4.1           htmltools_0.4.0         tools_3.6.3            
#>  [31] gtable_0.3.0            glue_1.4.1              dplyr_0.8.5            
#>  [34] Rcpp_1.0.4.6            carData_3.0-3           cellranger_1.1.0       
#>  [37] vctrs_0.3.0             gdata_2.18.0            nlme_3.1-144           
#>  [40] iterators_1.0.12        crosstalk_1.1.0.1       xfun_0.13              
#>  [43] stringr_1.4.0           openxlsx_4.1.5          mime_0.9               
#>  [46] miniUI_0.1.1.1          lifecycle_0.2.0         weights_1.0.1          
#>  [49] gtools_3.8.2            princurve_2.1.4         candisc_0.8-3          
#>  [52] MASS_7.3-51.5           scales_1.1.1            heplots_1.3-5          
#>  [55] hms_0.5.3               promises_1.1.0          parallel_3.6.3         
#>  [58] smacof_2.1-0            RColorBrewer_1.1-2      yaml_2.2.1             
#>  [61] curl_4.3                gridExtra_2.3           ggplot2_3.3.0          
#>  [64] rpart_4.1-15            reshape_0.8.8           latticeExtra_0.6-29    
#>  [67] stringi_1.4.6           foreach_1.5.0           plotrix_3.7-8          
#>  [70] e1071_1.7-3             checkmate_2.0.0         zip_2.0.4              
#>  [73] manipulateWidget_0.10.1 rlang_0.4.6             pkgconfig_2.0.3        
#>  [76] rgl_0.100.54            evaluate_0.14           lattice_0.20-38        
#>  [79] purrr_0.3.4             htmlwidgets_1.5.1       tidyselect_1.1.0       
#>  [82] plyr_1.8.6              magrittr_1.5            bookdown_0.19          
#>  [85] R6_2.4.1                generics_0.0.2          nnls_1.4               
#>  [88] Hmisc_4.4-0             pillar_1.4.4            haven_2.2.0            
#>  [91] foreign_0.8-75          survival_3.1-8          abind_1.4-5            
#>  [94] nnet_7.3-12             tibble_3.0.1            crayon_1.3.4           
#>  [97] car_3.0-7               wordcloud_2.6           plotly_4.9.2.1         
#> [100] ellipse_0.4.1           rmarkdown_2.1           jpeg_0.1-8.1           
#> [103] grid_3.6.3              readxl_1.3.1            data.table_1.12.8      
#> [106] forcats_0.5.0           digest_0.6.25           webshot_0.5.2          
#> [109] xtable_1.8-4            tidyr_1.0.3             httpuv_1.5.2           
#> [112] munsell_0.5.0           viridisLite_0.3.0