qqPlotFast {ramwas} | R Documentation |
Function qqPlotFast
creates a QQ-plot
with a confidence band and
an estimate of inflation factor lambda.
It optimized to work quickly even for tens of millions of p-values.
qqPlotPrepare( pvalues, ntests = NULL, ismlog10 = FALSE) qqPlotFast( x, ntests = NULL, ismlog10 = FALSE, ci.level = 0.05, ylim = NULL, newplot = TRUE, col = "#D94D4C", cex = 0.5, yaxmax = NULL, lwd = 3, axistep = 2, col.band = "#ECA538", makelegend = TRUE, xlab = expression( paste("\u2013", " log"[10]*"(", italic("P"), "), null")), ylab = expression( paste("\u2013", " log"[10]*"(", italic("P"), "), observed")))
pvalues |
Vector of p-values.
As is (if |
ntests |
If only significant p-values are provided,
the total number of tests performed. |
ismlog10 |
Specifies whether the provides p-values ( |
x |
Either a vector of p-values, as in |
ci.level |
Significance level of the confidence band.
Set to |
ylim |
Numeric vectors of length 2, giving the y coordinate range. Exactly as in Plotting Parameters. |
newplot |
If |
col |
The QQ-plot curve color. |
col.band |
Confidence band curve color. |
cex |
The size of QQ-plot points. As in Graphics Parameters. |
lwd |
The line width. |
axistep |
Distance between axis label ticks for both axis. |
yaxmax |
Maximum reach of the y axis. |
makelegend |
If true, add legend to the plot. |
xlab, ylab |
Axis labels. As in plot function. |
The function qqPlotFast
creates a QQ-plot.
The function qqPlotPrepare
extracts the necessary information
from a vector of p-values sufficient for creating QQ-plot.
The resulting object is many times smaller than the vector of p-values.
The function qqPlotPrepare
returns an object with
the necessary information from a vector of p-values
sufficient for creating QQ-plot.
The plot has no title. To add a title use title
.
The function works faster if the p-values are sorted.
Andrey A Shabalin andrey.shabalin@gmail.com
See vignettes: browseVignettes("ramwas")
.
# Million p-values n = 1e6 # Null p-values pv = runif(n) # QQ-plot should be nearly diagonal qqPlotFast(pv) title("QQ-plot") # Size of p-values before extraction of QQ-plot info object.size(pv) # Extract the QQ-plot info qq = qqPlotPrepare(pv) # Size of the QQ-plot info object object.size(qq) # Create QQ-plot, it is the same qqPlotFast(qq) # Create QQ-plot with plotting parameters qqPlotFast(qq, ylim = c(0,10), yaxmax = 9, axistep = 3, lwd = 3, cex = 1)