AmpliconDuo (version 1.1)

plotORdensity: Probability Density Plot Of Odds Ratios

Description

Plots for an ampliconduo data frame probability densities of the odds ratios of amplicon occurences in the two amplicon data sets. The function allows to shift the two extrema (odds ratios OR = 0 and OR = infinity) to the edges of the plot. Plots of multipe ampliconduo data frames are arranged in a 2-dimensional array with shared scales.

Usage

plotORdensity(x, log = "x", ncol = 2, adjust.zeroinf = TRUE, zero.pos = 0.005, 
inf.pos = 200, binwidth = 0.15, color = "black", xlab = "odds ratio", 
save = FALSE, path = NULL, file.name = NULL, format = "jpeg", ...)

Arguments

x

List or a single ampliconduo data frame, return value of the ampliconduo function.

log

Optional. Character specifying the variables to transform to log (“”,“x”, “y”, or “xy”). Default is “x”.

ncol

Optional. Integer value specifying the numer of columns used to arrange the plots. Default is 2.

adjust.zeroinf

Optional. Logical, specifies whether the density bar for 0 and inf should be shifted. Default value is TRUE.

zero.pos

Optional. Numeric, in case adjust.zeroinf is set to TRUE, determines the position for the odds ratio = 0 bar. Default value is 0.05.

inf.pos

Optional. Numeric, in case adjust.zeroinf is set to TRUE, gives the position for the odds ratio = inf bar. Default value is 200.

binwidth

Optional. Numeric, bin width to use, default is 0.15.

color

Optional. Character, name of the color used to draw the density bars. Default is “black”.

xlab

Optional. Character, label for the x-axis. Default is “odds ratio”.

save

Optional. Logical, TRUE to save the plot, else FALSE. Default 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_.”

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”.

...

Optional. Allows to pass other aesthetics.

See Also

qplot, used by plotAmpliconduo.set to create the plots.

facet_wrap, called for 2-dimensional arrangement of the plots.

ampliconduo, generates the input data.

Examples

## loads example data of ampliconduo data frames
data(amplicons)

## plot odds ratio density for amplicon frequencies in ampliconduo data frames
plotORdensity(amplicons)
plotORdensity(amplicons[1:4], binwidth = 0.1, color = "magenta")
plotORdensity(amplicons[[1]], binwidth = 0.1, color = "orange", main = "Sample FU25")
plotORdensity(amplicons[1:4],  color = "darkblue", ncol = 2, save = TRUE)