plotCurves: Plot Curves in an Orthogonal Matrix

In chipPCR: Toolkit of Helper Functions to Pre-Process Amplification Data

Description

Plots many curves on one plot in table-like fashion.

Usage

plotCurves(x, y, cyc = 1, fluo = 2:ncol(x), one.plot = FALSE, 
           nrow = ceiling(sqrt(ncol(y))), CPP = FALSE, ...)

Arguments

x	is the column of a data frame for the cycle or data.frame/matrix with whole data.
y	are multiple columns of fluorescence values from a data.frame (e.g., [, c(1:n)]).
cyc	is the index of column containing the cycle data. Used only if y is NULL.
fluo	are the columns containing the fluorescence data. Used only if y is NULL.
one.plot	logical, curves may be plotted on single chart (TRUE) or in matrix-like multiplot (FALSE).
nrow	number of rows in plot. Applies only if one.plot is FALSE.
CPP	logical, if TRUE CPP analysis is added to a plot. Ignored if one.plot is TRUE.
...	additional arguments to plot function.

Details

plotCurves is a function for the quick assessment of amplification curve raw data in an orthogonal matrix.

Value

None.

Author(s)

Stefan Roediger, Michal Burdukiewicz, Konstantin A. Blagodatskikh

Examples

# First example
plotCurves(VIMCFX96_60[, 1], VIMCFX96_60[, 2L:16], type = "l")

# Second example
y <- VIMCFX96_60[, 2L:16]
# Introduce some missing values.
y[c(1,4,5,6,23,34), c(2,4,9,15)] <- NA
plotCurves(VIMCFX96_60[, 1], y, nrow = 4, type = "l")

# Third example
# Same as second example but the CPP option is set to TRUE.
# Noise and missing values will be removed. 

y <- VIMCFX96_60[, 2L:16]
# Introduce some missing values.
y[c(1,4,5,6,23,34), c(2,4,9,15)] <- NA
plotCurves(VIMCFX96_60[, 1], y, nrow = 4, CPP = TRUE, type = "l")

# Fourth example
plotCurves(VIMCFX96_60, y = NULL, one.plot = TRUE, type = "l")
plotCurves(VIMCFX96_60, y = NULL, one.plot = FALSE, type = "l")

chipPCR documentation built on March 5, 2021, 9:06 a.m.