comparison goseq.r @ 7:67c29afac85f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 8e60c1cecc4561d61624799b0999e89687677ab1

6:07f6832bdd4d

  for (m in names(results)) {
    p <- results[[m]] %>%
      top_n(10, wt=-over_represented_pvalue)  %>%
      mutate(hitsPerc=numDEInCat*100/numInCat) %>%
      ggplot(aes(x=hitsPerc,
                   y=substr(term, 1, 40), # only use 1st 40 chars of terms otherwise squashes plot
                   colour=over_represented_pvalue,
                   size=numDEInCat)) +
      geom_point() +
      expand_limits(x=0) +
      labs(x="% DE in category", y="Category", colour="P value", size="Count", title=paste("Top over-represented categories in", cats_title), subtitle=paste(m, " method")) +
      theme(plot.title = element_text(hjust = 0.5), plot.subtitle = element_text(hjust = 0.5))
    print(p)
  }
  dev.off()
}

7:67c29afac85f

  for (m in names(results)) {
    p <- results[[m]] %>%
      top_n(10, wt=-over_represented_pvalue)  %>%
      mutate(hitsPerc=numDEInCat*100/numInCat) %>%
      ggplot(aes(x=hitsPerc,
                   y=reorder(substr(term, 1, 40), -over_represented_pvalue), # only use 1st 40 chars of terms otherwise squashes plot
                   colour=p.adjust.over_represented,
                   size=numDEInCat)) +
      geom_point() +
      expand_limits(x=0) +
      labs(x="% DE in category", y="Category", colour="Adj P value", size="Count", title=paste("Top over-represented categories in", cats_title), subtitle=paste(m, " method")) +
      theme(plot.title = element_text(hjust = 0.5), plot.subtitle = element_text(hjust = 0.5))
    print(p)
  }
  dev.off()
}