plotORdensity {AmpliconDuo} | R Documentation |
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, file.name = NULL, format = "jpeg", ...)
x |
List or a single ampliconduo data frame, return value of the |
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 |
zero.pos |
Optional. Numeric, in case |
inf.pos |
Optional. Numeric, in case |
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, |
path |
Optional. Character, in case the argument |
file.name |
Optional. If argument |
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. |
Anja Lange & Daniel Hoffmann
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 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)