plotCtRQ: Plot the relative quantification of Ct values from qPCR...

In HTqPCR: Automated analysis of high-throughput qPCR data

Description

Function for plotting the relative quantification (RQ) between two groups of data, whose Ct values have been tested for significant differential expression.

Usage

plotCtRQ(qDE, comparison = 1, genes, transform = "log2", p.val = 0.1, mark.sig = TRUE, p.sig = 0.05, p.very.sig = 0.01, mark.un = TRUE, un.tar = "black", un.cal = "black", col, legend = TRUE, xlim, mar, main, ...)

Arguments

qDE	list or data.frame, the result from ttestCtData or limmaCtData.
comparison	integer or character string, indicating which component to use if qDE is a list.
genes	numeric or character vector, selected genes to make the plot for.
transform	character string, how should the data be displayed. Options are "none", "log2" or "log10". See details
p.val	numeric between 0 and 1, if genes is not supplied all given with (adjusted) p-value below this threshold will be included.
mark.sig	logical, should significant features be marked.
p.sig	numeric, the cut-off for significant p-values that will be marked by *.
p.very.sig	numeric, the cut-off for very significant p-values that will be marked by ".
mark.un	logical, should data with unreliable target or calibrator samples be marked. See details.
un.tar	colour to use for the undetermined targets. See details.
un.cal	colour to use for the undetermined calibrators. See details.
col	vector, colours to use for the bars.
legend	logical, should a legend be included in the barplot.
xlim	vector of length 2, the limits on the x-axis. Mainly used for moving the legend to the left of bars.
mar	vector with 4 values, the size of the margins. See par for more info.
main	character string, the image title. Default to the name of the chosen comparison.
...	any other arguments will be passed to the barplot function.

Details

The relative quantification is calculated as RQ=2^-ddCT, where ddCT is the deltadeltaCt value.

If mark.un=TRUE, those bars where either the calibrator or target sample measurements were undetermined are marked using diagonal lines. Whether either of these are called undetermined (includes unreliable values) or not depends on all the input Ct values in ttestCtData or limmaCtData, and whether stringent=TRUE was used in these functions.

Value

A plot is created on the current graphics device.

Author(s)

Heidi Dvinge

See Also

ttestCtData and limmaCtData for testing the Ct data for differential expression.

HTqPCR documentation built on Nov. 8, 2020, 6:51 p.m.