plotROC collapsing ROC curves into single line
Entering edit mode
Last seen 3.8 years ago

Hi all,

I'm using Anaquin to measure detection of Sequin fold change by a sequencer. The fold change is between Sequin mixes A and B. When I try to make a ROC plot using the following parameters: - Expected log fold change - 1 minus P-value of measurement - TP/FP label of measurement plotROC collapses all the curves, each one representing a different level of fold change, into a single curve. Adding to the problem the curve is also a "perfect" right-angle. I've tried using multiple definitions of a true positive including P < 0.05, P < 0.001 and Q < 0.05, but I still have the issue.

Here's the code I've been using:

# Title
title <- 'ROC gene plot - Illumina'
# Sequin names
seqs <- row.names(exp_gene_sequins)
# Expected log fold
ratio <- exp_gene_sequins$Int_Log2_Fold_change
# How the ROC points are ranked (scoring function)
score <- 1 - illumina_gene_sequins$pvalue
# Classified labels (TP/FP)
label <- illumina_gene_sequins$Label
# Make the plot
plotROC(seqs, score, ratio, label, title=title, refGroup=0, legTitle = "Fold change")

Summary plotROC function bunches all fold changes together into a single line

Many thanks, Will

anaquin plotroc • 399 views

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