diff --git a/vignettes/SIAMCAT_holdout.Rmd b/vignettes/SIAMCAT_holdout.Rmd index 2b0266d8..c1aee872 100755 --- a/vignettes/SIAMCAT_holdout.Rmd +++ b/vignettes/SIAMCAT_holdout.Rmd @@ -208,33 +208,7 @@ model.evaluation.plot('FR-CRC'=siamcat.fr, colours=c('dimgrey', 'orange')) ``` - -```{r eval_plot_hidden, fig.width = 6, fig.asp=1, fig.align="left", echo=FALSE} - -args <- list('FR-CRC'=siamcat.fr, 'CN-CRC'=siamcat.cn) - -colours=c('dimgrey', 'orange') - -plot(NULL, xlim = c(0, 1), ylim = c(0, 1), - xlab = "False positive rate", ylab = "True positive rate", - type = "n") -title(paste("ROC curve for the model", sep = " ")) -abline(a = 0, b = 1, lty = 3) - -legend.val <- c() -for (i in 1:length(args)) { - legend.val <- c(legend.val, - as.numeric(SIAMCAT:::single.roc.plot(args[[i]], colours[i], - show.all=FALSE, verbose=0))) -} - -legend('bottomright', - legend= paste0(names(args), - ' AUC: ' , - format(legend.val, digits=3)), - col=colours, lty=1, lwd=2, cex=0.8, y.intersp=1.5) - -``` +![](./eval_plot_holdout.png) # Session Info diff --git a/vignettes/SIAMCAT_vignette.Rmd b/vignettes/SIAMCAT_vignette.Rmd index 44969105..eeb1ffc3 100755 --- a/vignettes/SIAMCAT_vignette.Rmd +++ b/vignettes/SIAMCAT_vignette.Rmd @@ -238,10 +238,12 @@ To plot the results of the evaluation, we can use the function `model.evaluation.plot`, which produces a pdf-file showing the ROC and PR Curves for the different resamples runs as well as the mean ROC and PR Curve. -```{r eval_plot, fig.height=6, fig.width=6, fig.align='left', message=FALSE} +```{r eval_plot, eval=FALSE} model.evaluation.plot(siamcat) ``` +![](./eval_plot.png) + ## Interpretation Plot The final plot produced by `SIAMCAT` is the model interpretation plot, created diff --git a/vignettes/eval_plot.png b/vignettes/eval_plot.png new file mode 100644 index 00000000..0115dbb7 Binary files /dev/null and b/vignettes/eval_plot.png differ diff --git a/vignettes/eval_plot_holdout.png b/vignettes/eval_plot_holdout.png new file mode 100644 index 00000000..7b751c67 Binary files /dev/null and b/vignettes/eval_plot_holdout.png differ