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Last data update: 2014.03.03

R: Frequency-Frequency Plot Focusing On Significant Deviations...

plotAmpliconduo

R Documentation

Frequency-Frequency Plot Focusing On Significant Deviations In Amplicon Occurences

Description

Applied to an ampliconduo data frame, one element of the return value of the ampliconduo function. Generates a plot of freqB over freqA (the read numbers of the same amplicon in both halves A and B of a split sample). For amplicons that have significantly deviating read numbers, i.e. with a p-value or adjusted p-value below a certain treshold, points are colored differently (default: red).

Usage

plotAmpliconduo(x, color.treshold = 0.05, xlab = "Abundance (PCR A)", 
ylab = "Abundance (PCR B)",main = NULL, log = "xy", corrected = TRUE, asp = 1, 
legend.position = NULL, save = FALSE, path = NULL, file.name = NULL,
format = "jpeg", h.start = 0, ...)

Arguments

`x`	Ampliconduo data frame, an element of the returned list of the `ampliconduo` function.
`color.treshold`	Optional. Numeric value specifying at which p-value or adjusted p-value points in the plot are drawn in complementary color. Default value is 0.05.
`xlab`	Optional. Character indicating the x-axis label. Default is “Abundance (PCR A)”.
`ylab`	Optional. Character indicating the y-axis label. Default is “Abundance (PCR B)”.
`main`	Optional. Character specifying the overall title of the plot. If no value is passed, takes the sample name from the `x$sample` column.
`log`	Optional. Character specifying the variables to transform to log (“”,“x”, “y”, or “xy”). Default is “xy”.
`corrected`	Optional. Logical to decide whether the p-value (`FALSE`), or corrected p-value (`TRUE`) is used for coloring. Default value is `TRUE`.
`asp`	Optional. Numeric value, the y/x aspect ratio. Default is 1.
`legend.position`	Optional. Numeric vector of length two. Defines the position of the legend. By default tries to find a position that fits best the arrangement of the plots.
`save`	Optional. Logical value indicationg if the plot should be saved to file. Default value is `FALSE`.
`path`	Optional. Character, in case the argument `save` was set to `TRUE`, specifies the directory (no backslash or slash at the end) for saving. By default (parameter `save` is set to TRUE) the plot is saved in the working directory.
`file.name`	Optional. If argument `save` was set to `TRUE` specifies the file name for the plot. The default name is “ampliconduo_<date>.<file extension>”
`format`	Optional. Character specifying the format of the saved file. One of “eps”, “ps”, “tex”, “pdf”, “jpeg”, “tiff”, “png”, “bmp”, “svg” and “wmf” (windows only). Default format is “jpeg”.
`h.start`	Optional. Numeric value between 0 and 360 defines the color of the plotted points. Default value is 0 (blue-green, red).
`...`	Optional. Allows to pass other aesthetics.

Author(s)

Anja Lange & Daniel Hoffmann

References

http://had.co.nz/ggplot2/book/qplot.pdf

Examples

## load example data
data(amplicons)

## extract the second ampliconduo data frame
ampliconduo2 <- amplicons[[2]]

## plot the amplicon frequencies of the ampliconduo data frame 
plotAmpliconduo(ampliconduo2, main = "ampliconduo_2")
plotAmpliconduo(ampliconduo2, main = "ampliconduo_2", h.start = 50, log = "")
plotAmpliconduo(ampliconduo2, h.start = 50, log = "", asp = 2, corrected = FALSE)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(AmpliconDuo)
Loading required package: ggplot2
Loading required package: xtable
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/AmpliconDuo/plotAmpliconduo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotAmpliconduo
> ### Title: Frequency-Frequency Plot Focusing On Significant Deviations In
> ###   Amplicon Occurences
> ### Aliases: plotAmpliconduo
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ## load example data
> data(amplicons)
> 
> ## extract the second ampliconduo data frame
> ampliconduo2 <- amplicons[[2]]
> 
> ## plot the amplicon frequencies of the ampliconduo data frame 
> plotAmpliconduo(ampliconduo2, main = "ampliconduo_2")
> plotAmpliconduo(ampliconduo2, main = "ampliconduo_2", h.start = 50, log = "")
> plotAmpliconduo(ampliconduo2, h.start = 50, log = "", asp = 2, corrected = FALSE)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>