Plot logistic model for sequins

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Description

Create a scatter plot with input concentration on the x-axis, and measured proportion on the y-axis.

Usage

1
plotLogistic(data, title, xlab, ylab, showLOA, threshold, ...)

Arguments

data

Anaquin dataset created by AnaquinData. It needs to define information in Details.

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)

...

Reserved for internal testing

Details

plotLogistic requires the following data inputs from AnaquinData.

seqs List of sequin identifiers (eg. R2_11_2).
input Input concentration of sequins in attomol/ul.
measured Measured variable (eg: sensitivity).

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 GLM 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.

Value

The functions does not return anything but it prints a scatter plot with a fitted logistic function.

Author(s)

Ted Wong t.wong@garvan.org.au

Examples

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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
input <- log2(UserGuideData_5.4.5.1$InputConcent)

# Measured sensitivity
measured <- UserGuideData_5.4.5.1$Sn

anaquin <- AnaquinData(analysis='PlotLogistic',
                           seqs=seqs,
                          input=input,
                       measured=measured)

plotLogistic(anaquin, title=title, xlab=xlab, ylab=ylab, showLOA=TRUE)