svm validation, tensorflow mp2d pa predictions, r results removed, cleanup

1 files changed, 23 insertions, 0 deletions

diff --git a/scripts/pa-groups.R b/scripts/pa-groups.R
new file mode 100755
index 0000000..005dd3d
--- /dev/null
+++ b/scripts/pa-groups.R
@@ -0,0 +1,23 @@
+#!/usr/bin/env Rscript
+library(ggplot2)
+data <- read.csv("tables/pa-table.csv")
+for (i in c(2:10)) {
+  name <- names(data)[i]
+  group <- data[data[i] == 1,c(15,19,20,21,22)]
+  freq <- 100*colSums(group,na.rm=TRUE)/colSums(!is.na(group))
+  plot <- ggplot(data.frame(freq),aes(x=c("lazar","LR-sgd","LR-scikit","NN","RF"),y=freq)) + geom_bar(stat="identity") + ylab("% mutagenic") + xlab(name) + ylim(c(0,100))
+  ggsave(paste("figures/",name,".png",sep=""))
+}
+#groups <- names(data)[c(2:10)]
+#labels <- data$Mutagenicity
+#data$Mutagenicity <- NULL
+#m <- as.matrix(data)
+#dist <- as.dist(m)
+#tsne <- Rtsne(dist,is_distance=T)
+#write.csv(tsne,"tsne.csv")
+#write.csv(data.frame(x = tsne$Y[,1], y = tsne$Y[,2]),"tsne.csv")
+#tsne_plot <- data.frame(x = tsne$Y[,1], y = tsne$Y[,2])
+#colors <- c("PA" = "#00BFC4", "mutagen" = "#F8766D", "non-mutagen" = "#7CAE00")
+#plot <- ggplot(tsne_plot)
+#plot + geom_point(aes(x=x, y=y, color = labels)) + xlab(element_blank()) + ylab(element_blank()) + theme(axis.ticks = element_blank(), axis.text = element_blank(), legend.title=element_blank()) + scale_color_manual(values = colors)
+#ggsave("figures/tsne-mp2d.png")