#### Select a combination of recountIDs, classifiers and suffixes ####
tests <- expand.grid(
classifier = c("knn", "rf", "svm"),
recountID = recountIDs <- c("SRP042620",
"SRP056295",
"SRP061240",
"SRP062966"),
data.type = "log2norm",
suffix = c("allvars.tsv")
)
## Tester
tests$files <- file.path("results",
tests$recountID,
tests$classifier,
"tables",
paste(sep="_", tests$classifier,
# "_", tests$recountID,
tests$data.type,
tests$suffix))
tests$perm.files <- sub(pattern = ".tsv", replacement = "_permLabels.tsv", x = tests$files)
#### Select experiments for which both real data and permuted labels files exist ####
tests$both.files.ok <- file.exists(tests$files) & file.exists(tests$perm.files)
# View(tests)
#### Read error tables ####
error.summary <- SummarizeErrorTable(tests$files, stopIfMissing = FALSE)
perm.error.summary <- SummarizeErrorTable(tests$perm.files, stopIfMissing = FALSE)
#### Plot comparing error rates with real and permuted labels ####
#names(tests)
colors.per.classifier <- c("knn" = "blue",
"svm" = "brown",
"rf" = "darkgreen")
tests$color <- colors.per.classifier[as.vector(tests$classifier)]
pch.per.recountID <- c("SRP042620" = 1,
"SRP056295" = 2,
"SRP061240" = 3,
"SRP062966" = 4)
tests$pch <- pch.per.recountID[as.vector(tests$recountID)]
tests[, c("classifier", "color")]
plot(error.summary$testing.error.rate,
perm.error.summary$testing.error.rate,
xlim = c(0,1), ylim = c(0,1),
xlab = "Error rate",
ylab = "Error rate, permuted lables",
col = tests$color,
pch = tests$pch,
panel.first = c(grid(),
abline(a=0,b=1, col="grey")))
legend("bottomright",
legend=names(pch.per.recountID),
pch=pch.per.recountID)
legend("topright",
legend=names(colors.per.classifier),
col=colors.per.classifier,
pch=1)
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