# Plot Results Circular Permutation QQ plots ```r plot_results(results="",by="",plot_all=TRUE, var = "", save_plot=TRUE, plot_name="", bf= FALSE , save_qq = TRUE) ``` ## Arguments - `results`: Results datarame from "get_results()" - `by`: Visualize results by "trait" OR by "set" - `plot_all`: plot_all = TRUE plots all the variables in the results dataframe and saves a pdf file in the working directory. Setting plot_all to FALSE plots a single variable(trait or set). The argument "var" must be declared. - `var`: Variable name to plot - `save_plot`: save_plot = TRUE saves the plots in the working directory. save_plot = FALSE the plot is visualized at the console. save_plot = FALSE can be used only when plot_all is set to FALSE. The plot displayed at the console is interactive, clicking on a point displays the points name. - `plot_name`: Argument used to save the file name for the plots. Default value = Results_genomicper_[set/trait] - `bf`: Displays the bonferroni correction - `save_qq`: TRUE returns the qq plot values ## Returns - **qq**: Data frame with qq plot values ## See Also `get_results` ## Examples ```r data(demo,SNPsAnnotation) all_data <- read_pvals(data_name=demo,snps_ann=SNPsAnnotation) genome_results <-genome_order(all_data=all_data) # Results from genome_order ordered_alldata <- genome_results$ordered_alldata gs_locs <- genome_results$gs_locs # Create new environment to save the data: gper.env <- new.env() # Load Pathways data(RHSA164843,RHSA446343,RHSA8876384,RHSA8964572,RHSA109582,RHSA1474244,envir=gper.env) paths_res <- read2_paths(ordered_alldata=ordered_alldata,gs_locs=gs_locs, sets_from="workspace",sets_prefix="RHSA",level="snp",envir=gper.env) pers_ids <- paths_res$per_ors pathways<- paths_res$pathways snps_permutation(ordered_alldata=ordered_alldata,pers_ids=pers_ids, ntraits=c(7,9),nper=10,saveto="workspace",threshold=0.05, gs_locs=gs_locs,envir = gper.env) results <- get_results(res_pattern="Permus",level="snp", from="workspace",threshold=0.05,envir = gper.env) #saves plots to working directory ## Not run: qq <- plot_results(results=results,by="set",plot_all=TRUE) qq <- plot_results(results=results,by="trait",plot_all=FALSE,var="trait1") qq <- plot_results(results=results,by="set", plot_all=FALSE,var="R-HSA-8964572", save_plot=FALSE) ## IMPORTANT: to EXIT interactive plot ## right click on the plot to stop ## End(Not run) ```

plot_results function