plotLogistic: Plot logistic model for sequins

Description Usage Arguments Details Value Author(s) Examples

View source: R/plotLogistic.R

Description

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

Usage

1
plotLogistic(seqs, x, y, title, xlab, ylab, showLOA, threshold)

Arguments

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).

Details

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.

Value

The function returns the limit of quantification.

Author(s)

Ted Wong [email protected]

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
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)

Anaquin documentation built on Nov. 17, 2017, 1:02 p.m.