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_.
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.