plot.FDX | R Documentation |
FDX
objectsPlots raw p-values of a FDX
object and highlights rejected and
accepted p-values. If present, the critical values are plotted, too.
## S3 method for class 'FDX' plot( x, col = c(2, 4, 1), pch = c(1, 1, 1), lwd = c(1, 1, 1), type.crit = "b", legend = NULL, ... )
x |
an object of class " |
col |
a numeric or character vector of length 3 indicating the colors of the
|
pch |
a numeric or character vector of length 3 indicating the point characters of the
|
lwd |
a numeric vector of length 3 indicating the thickness of the points and lines. |
type.crit |
1-character string giving the type of plot desired for the
critical values (e.g.: |
legend |
if NULL, no legend is plotted; otherwise expecting a character string like "topleft" etc. or a numeric vector of two elements indicating (x, y) coordinates. |
... |
further arguments to |
If x
contains results of a weighted approach, the Y-axis of the plot
is derived from the weighted p-values. Otherwise, it is constituted by the
raw ones.
X1 <- c(4, 2, 2, 14, 6, 9, 4, 0, 1) X2 <- c(0, 0, 1, 3, 2, 1, 2, 2, 2) N1 <- rep(148, 9) N2 <- rep(132, 9) Y1 <- N1 - X1 Y2 <- N2 - X2 df <- data.frame(X1, Y1, X2, Y2) df # Construction of the p-values and their supports (fisher.pvalues.support # is from 'DiscreteFDR' package!) df.formatted <- fisher.pvalues.support(counts = df, input = "noassoc") raw.pvalues <- df.formatted$raw pCDFlist <- df.formatted$support DLR.sd.fast <- DLR(raw.pvalues, pCDFlist) DLR.sd.crit <- DLR(raw.pvalues, pCDFlist, critical.values = TRUE) DLR.su.fast <- DLR(raw.pvalues, pCDFlist, direction = "su") DLR.su.crit <- DLR(raw.pvalues, pCDFlist, direction = "su", critical.values = TRUE) plot(DLR.su.fast) plot(DLR.su.crit, xlim = c(1, 5), ylim = c(0, 0.4)) plot(DLR.sd.fast, col = c(2, 4), pch = c(2, 3), lwd = c(2, 2), legend = "topleft", xlim = c(1, 5), ylim = c(0, 0.4)) plot(DLR.sd.crit, col = c(2, 4, 1), pch = c(1, 1, 4), lwd = c(1, 1, 2), type.crit = 'o', legend = c(1, 0.4), lty = 1, xlim = c(1, 5), ylim = c(0, 0.4))
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