plotORdensity {AmpliconDuo}R Documentation

Probability Density Plot Of Odds Ratios


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.


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, = NULL, format = "jpeg", ...)



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


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


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


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


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


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


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


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


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


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


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.

Optional. If argument save was set to TRUE specifies the file name for the plot. The default name is “ampliconduo_<date>.<file extension>”


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.


Anja Lange & Daniel Hoffmann

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.


## loads example data of ampliconduo data frames

## plot odds ratio density for amplicon frequencies in ampliconduo data frames
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)

[Package AmpliconDuo version 1.1.1 Index]