plotLogistic {Anaquin} | R Documentation |
Create a scatter plot with input concentration on the x-axis, and measured proportion on the y-axis.
plotLogistic(seqs, x, y, title, xlab, ylab, showLOA, threshold)
seqs |
Sequin names |
x |
Expected input concentration on the x-axis |
y |
Measured proportion on the y-axis |
title |
Title of the plot. (Default to NULL). |
xlab |
Label for the x-axis. (Default to NULL). |
ylab |
Label for the y-axis. (Default to NULL). |
showLOA |
Display limit-of-assembly. (Default to TRUE). |
threshold |
Threshold required for limit-of-assembly (LOA). (Default to 0.7). |
The plotLogistic
function creates a scatter plot with input
concentration on the x-axis, and measured proportion on the y-axis. Common
measured statistics include p-value, percentage and sensitivity. The plot
builds a logistic regression model between the two variables.
The function also estimates limit-of-assembly (LOA) breakpoint, and reports it on the plot if found. The LOA breakpoint is an empirical detection limit, and also the abundance whereby the fitted logistic curve exceeds a user-defined threshold.
The function returns the limit of quantification.
Ted Wong t.wong@garvan.org.au
library(Anaquin) # # Data set generated by Cufflinks and Anaquin. described in Section 5.4.5.1 of # the user guide. # data(UserGuideData_5.4.5.1) title <- 'Assembly Plot' xlab <- 'Input Concentration (log2)' ylab <- 'Sensitivity' # Sequin names seqs <- row.names(UserGuideData_5.4.5.1) # Input concentration x <- log2(UserGuideData_5.4.5.1$Input) # Measured sensitivity y <- UserGuideData_5.4.5.1$Sn plotLogistic(seqs, x, y, title=title, xlab=xlab, ylab=ylab, showLOA=TRUE)