MVP.Report.QQplot {rMVP} | R Documentation |
QQ Plot
MVP.Report.QQplot(P.values, taxa_name, col = c("blue"), cex = 0.5, threshold = NULL, amplify = TRUE, signal.col = "red", signal.pch = 19, signal.cex = 0.8, conf.int = TRUE, cex.axis = 1, conf.int.col = "grey", threshold.col = "red", outpath = getwd(), file.type = "jpg", memo = "MVP", box = TRUE, dpi = 300, file.output = TRUE, verbose = TRUE)
P.values |
P values |
taxa_name |
The identifier of the phenotype will be used to generate a portion of the image file name. If the title parameter is NULL, it will also be part of the title. |
col |
default color is "blue" |
cex |
A numerical value giving the amount by which plotting text and
symbols should be magnified relative to the default. This starts as 1
when a device is opened, and is reset when the layout is changed, e.g.
by setting mfrow. see |
threshold |
Number or Vector. The cutoff line on Manhattan plot, e.g. Bonfferoni correction. More than one significant line can be added onto one figure. If threshold=0 or NULL, the threshold line will not be added. |
amplify |
Logical value. If TRUE, the points that passed the threshold line will be highlighted |
signal.col |
Character. If "amplify" is TRUE, "signal.col" is used to set the color of significant points, if "signal.col" is NULL, the colors of significant points will not be changed |
signal.pch |
Number. If "amplify" is TRUE, users can set the type of significant points |
signal.cex |
Number. If "amplify" is TRUE, "signal.cex" is used to set the size of significant points |
conf.int |
Whether to draw a confidence interval |
cex.axis |
a number, controls the size of numbers of X-axis and the size of labels of circle plot. |
conf.int.col |
a character, the color of the confidence interval on QQ-plot. |
threshold.col |
Character or Vector. The colors of threshold lines |
outpath |
Only when file.output = TRUE, determines the path of the output file |
file.type |
A string or NULL is used to determine the type of output
file. Can be "jpg", "pdf", "tiff". If it is NULL, it will use
|
memo |
the prefix of the output image file. |
box |
A Boolean value that controls whether to draw a box around QQplot. |
dpi |
a number, the picture element for .jpg and .tiff files. The default is 300. |
file.output |
Logical value. If TRUE, the figures will be generated. |
verbose |
whether to print detail. |
Output file: <memo>.QQplot.<taxa_name>.<type>
data(pig60K, package = "rMVP") MVP.Report(pig60K, plot.type="q", file.output=FALSE)