In jakubkala/QuiPTsim:

knitr::opts_chunk$set(echo = TRUE)
source("../inst/unbalanced-experiments.R")

Report details

print(paste0("Experiment name: ", experiment_name))

Time

ranking_results_lm %>%
  ggplot(aes_string(x="n_kmers", y=paste0(metrics, "_mean"))) +
  geom_line(aes_string(linetype="Filter", group="Filter", color="Filter"), size = 1) +
  geom_point(data = nonranking_results_lm, mapping = aes_string(x="n_kmers", y=paste0(metrics, "_mean"), shape="Filter"), size=4) +
  facet_wrap(~Fraction, ncol=ncol) +
  scale_x_continuous(name="Number of selected k-mers",  trans='log2') +
  scale_linetype_manual(values=rep(c("solid", "dotdash"), each=5)) +
  scale_color_manual(values=rep(c('#e41a1c','#377eb8','#4daf4a','#984ea3','#ff7f00'), 3)) +
  scale_shape_manual(values=c(8, 15:18)) + 
  ylab(metrics)

ggsave(paste0("plots/", exp_prefix, "_results_AUC.pdf"))

cat(paste0("\\begin{figure}\n",
    "\\centering\n",
    "\\includegraphics[scale=0.52]{sections/plots/", exp_prefix,"_results_AUC.pdf}\n",
    "\\caption{", experiment_name, " - averaged AUC score for each k-mer filtering method presented for regularized logistic regression. For nonranking methods, number of selected k-mers is averaged over all experiment iterations.}\n",
    "\\label{fig:", exp_prefix,"_results_AUC}\n",
    "\\end{figure}"))

jakubkala/QuiPTsim documentation built on Jan. 17, 2022, 11:27 p.m.