## ---- echo = FALSE-------------------------------------------------------------------------------- options(width = 100) ## ------------------------------------------------------------------------------------------------- library(iCOBRA) data(cobradata_example) class(cobradata_example) cobradata_example ## ------------------------------------------------------------------------------------------------- cobradata_example <- calculate_adjp(cobradata_example) ## ------------------------------------------------------------------------------------------------- cobraperf <- calculate_performance(cobradata_example, binary_truth = "status", cont_truth = "logFC", splv = "none", maxsplit = 4) slotNames(cobraperf) ## ------------------------------------------------------------------------------------------------- cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = "Dark2", facetted = TRUE) ## ---- fig.width = 7, fig.height = 4, fig.cap = "", warning = FALSE-------------------------------- plot_tpr(cobraplot) ## ---- fig.width = 7, fig.height = 4, fig.cap = "", warning = FALSE-------------------------------- plot_fdrtprcurve(cobraplot) ## ---- fig.width = 7, fig.height = 4, fig.cap = "", warning = FALSE-------------------------------- plot_overlap(cobraplot) ## ---- fig.width = 7, fig.height = 5, warning = FALSE---------------------------------------------- cobraperf <- calculate_performance(cobradata_example, binary_truth = "status", cont_truth = "status", splv = "expr_cat") cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = "Dark2", facetted = TRUE) plot_tpr(cobraplot) ## ---- fig.width = 7, fig.height = 5, warning = FALSE---------------------------------------------- library(ggplot2) pp <- plot_tpr(cobraplot, stripsize = 7.5, pointsize = 3) pp + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1, size = 10), axis.text.y = element_text(size = 10), axis.title.x = element_text(size = 10), axis.title.y = element_text(size = 10)) ## ---- fig.width = 7, fig.height = 4, warning = FALSE---------------------------------------------- pp + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1, size = 10), axis.text.y = element_text(size = 10), axis.title.x = element_text(size = 10), axis.title.y = element_text(size = 10), legend.position = "bottom") + facet_wrap(~splitval, nrow = 1) ## ---- fig.width = 7, fig.height = 5, warning = FALSE---------------------------------------------- plot_overlap(cobraplot) plot_overlap(cobraplot, cex = c(1, 0.7, 0.7)) ## ---- fig.width = 7, fig.height = 5, warning = FALSE---------------------------------------------- cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = c("blue", "green", "pink"), facetted = TRUE) pp <- plot_tpr(cobraplot, stripsize = 7.5, pointsize = 3) pp + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1, size = 10), axis.text.y = element_text(size = 10), axis.title.x = element_text(size = 10), axis.title.y = element_text(size = 10)) ## ---- eval = FALSE-------------------------------------------------------------------------------- # COBRAapp(cobradata_example) # COBRAapp() ## ------------------------------------------------------------------------------------------------- COBRAData_to_text(cobradata = cobradata_example, truth_file = "cobradata_truth.txt", result_files = "cobradata_results.txt", feature_id = "feature") ## ------------------------------------------------------------------------------------------------- cobra <- COBRAData_from_text(truth_file = "cobradata_truth.txt", result_files = "cobradata_results.txt", feature_id = "feature") cobra