[R-gregmisc-users] SF.net SVN: r-gregmisc:[1646] trunk/gplots
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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1646] trunk/gplots
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From: <wa...@us...> - 2013-03-24 05:19:07
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Revision: 1646
http://sourceforge.net/p/r-gregmisc/code/1646
Author: warnes
Date: 2013-03-24 05:19:04 +0000 (Sun, 24 Mar 2013)
Log Message:
-----------
Add ci.width argument to barplot2() to allow varying the length of the 't' at the end of confidence interval bars.
Modified Paths:
--------------
trunk/gplots/R/barplot2.R
trunk/gplots/man/barplot2.Rd
Modified: trunk/gplots/R/barplot2.R
===================================================================
--- trunk/gplots/R/barplot2.R 2013-03-24 04:50:22 UTC (rev 1645)
+++ trunk/gplots/R/barplot2.R 2013-03-24 05:19:04 UTC (rev 1646)
@@ -12,30 +12,60 @@
barplot2 <- function(height, ...) UseMethod("barplot2")
barplot2.default <-
- function(
- height,
- width = 1,
- space = NULL,
- names.arg = NULL,
- legend.text = NULL,
- beside = FALSE,
- horiz = FALSE,
- density = NULL,
- angle = 45,
- col = NULL,
- prcol = NULL,
- border = par("fg"),
- main = NULL,
- sub = NULL, xlab = NULL, ylab = NULL,
- xlim = NULL, ylim = NULL, xpd = TRUE, log = "",
- axes = TRUE, axisnames = TRUE,
- cex.axis = par("cex.axis"), cex.names = par("cex.axis"),
- inside = TRUE, plot = TRUE, axis.lty = 0, offset = 0,
- plot.ci = FALSE, ci.l = NULL, ci.u = NULL,
- ci.color = "black", ci.lty = "solid", ci.lwd = 1,
- plot.grid = FALSE, grid.inc = NULL,
- grid.lty = "dotted", grid.lwd = 1, grid.col = "black",
- add = FALSE, panel.first = NULL, panel.last = NULL, ...)
+ function(
+ height,
+ width = 1,
+ space = NULL,
+ names.arg = NULL,
+ legend.text = NULL,
+ beside = FALSE,
+ horiz = FALSE,
+ density = NULL,
+ angle = 45,
+ col = NULL,
+ prcol = NULL,
+ border = par("fg"),
+ main = NULL,
+ sub = NULL,
+ xlab = NULL,
+ ylab = NULL,
+
+ xlim = NULL,
+ ylim = NULL,
+ xpd = TRUE,
+ log = "",
+
+ axes = TRUE,
+ axisnames = TRUE,
+
+ cex.axis = par("cex.axis"),
+ cex.names = par("cex.axis"),
+
+ inside = TRUE,
+ plot = TRUE,
+ axis.lty = 0,
+ offset = 0,
+
+ plot.ci = FALSE,
+ ci.l = NULL,
+ ci.u = NULL,
+
+ ci.color = "black",
+ ci.lty = "solid",
+ ci.lwd = 1,
+ ci.width = 0.5,
+
+ plot.grid = FALSE,
+ grid.inc = NULL,
+
+ grid.lty = "dotted",
+ grid.lwd = 1,
+ grid.col = "black",
+
+ add = FALSE,
+ panel.first = NULL,
+ panel.last = NULL,
+ ...)
{
if (!missing(inside)) .NotYetUsed("inside", error = FALSE)# -> help(.)
@@ -137,10 +167,10 @@
# Check for NA values and issue warning if required
height.na <- sum(is.na(height))
if (height.na > 0)
- {
+ {
warning(sprintf("%.0f values == NA in 'height' omitted from logarithmic plot",
height.na), domain = NA)
- }
+ }
# Check for 0 values and issue warning if required
# _FOR NOW_ change 0's to NA's so that other calculations are not
@@ -148,15 +178,15 @@
# except for stacked bars, so don't change those.
height.lte0 <- sum(height <= 0, na.rm = TRUE)
if (height.lte0 > 0)
- {
+ {
warning(sprintf("%0.f values <=0 in 'height' omitted from logarithmic plot",
height.lte0), domain = NA)
-
+
# If NOT stacked bars, modify 'height'
if (beside)
height[height <= 0] <- NA
- }
-
+ }
+
if (plot.ci && (min(ci.l) <= 0))
stop("log scale error: at least one lower c.i. value <= 0")
@@ -172,12 +202,12 @@
{
rectbase <- c(height[is.finite(height)], ci.l)
rectbase <- min(0.9 * rectbase[rectbase > 0])
- }
+ }
else
{
rectbase <- height[is.finite(height)]
rectbase <- min(0.9 * rectbase[rectbase > 0])
- }
+ }
# if axis limit is set to < above, adjust bar base value
# to draw a full bar
@@ -253,7 +283,7 @@
# Execute the panel.first expression. This will work here
# even if 'add = TRUE'
panel.first
-
+
# Set plot region coordinates
usr <- par("usr")
@@ -335,23 +365,23 @@
# Execute the panel.last expression here
panel.last
-
+
if (plot.ci)
{
# CI plot width = barwidth / 2
- ci.width = width / 4
+ half.ci.width = width * ci.width / 2
if (horiz)
{
segments(ci.l, w.m, ci.u, w.m, col = ci.color, lty = ci.lty, lwd = ci.lwd)
- segments(ci.l, w.m - ci.width, ci.l, w.m + ci.width, col = ci.color, lty = ci.lty, lwd = ci.lwd)
- segments(ci.u, w.m - ci.width, ci.u, w.m + ci.width, col = ci.color, lty = ci.lty, lwd = ci.lwd)
+ segments(ci.l, w.m - half.ci.width, ci.l, w.m + half.ci.width, col = ci.color, lty = ci.lty, lwd = ci.lwd)
+ segments(ci.u, w.m - half.ci.width, ci.u, w.m + half.ci.width, col = ci.color, lty = ci.lty, lwd = ci.lwd)
}
else
{
segments(w.m, ci.l, w.m, ci.u, col = ci.color, lty = ci.lty, lwd = ci.lwd)
- segments(w.m - ci.width, ci.l, w.m + ci.width, ci.l, col = ci.color, lty = ci.lty, lwd = ci.lwd)
- segments(w.m - ci.width, ci.u, w.m + ci.width, ci.u, col = ci.color, lty = ci.lty, lwd = ci.lwd)
+ segments(w.m - half.ci.width, ci.l, w.m + half.ci.width, ci.l, col = ci.color, lty = ci.lty, lwd = ci.lwd)
+ segments(w.m - half.ci.width, ci.u, w.m + half.ci.width, ci.u, col = ci.color, lty = ci.lty, lwd = ci.lwd)
}
}
Modified: trunk/gplots/man/barplot2.Rd
===================================================================
--- trunk/gplots/man/barplot2.Rd 2013-03-24 04:50:22 UTC (rev 1645)
+++ trunk/gplots/man/barplot2.Rd 2013-03-24 05:19:04 UTC (rev 1646)
@@ -84,8 +84,8 @@
axes = TRUE, axisnames = TRUE,
cex.axis = par("cex.axis"), cex.names = par("cex.axis"),
inside = TRUE, plot = TRUE, axis.lty = 0, offset = 0,
- plot.ci = FALSE, ci.l = NULL,
- ci.u = NULL, ci.color = "black", ci.lty = "solid", ci.lwd = 1,
+ plot.ci = FALSE, ci.l = NULL, ci.u = NULL,
+ ci.color = "black", ci.lty = "solid", ci.lwd = 1, ci.width = 0.5,
plot.grid = FALSE, grid.inc = NULL,
grid.lty = "dotted", grid.lwd = 1, grid.col = "black",
add = FALSE, panel.first = NULL, panel.last = NULL, \dots)
@@ -176,7 +176,10 @@
the same dim structure as \code{height}.}
\item{ci.color}{the color for the confidence interval line segments}
\item{ci.lty}{the line type for the confidence interval line segments}
- \item{ci.lwd}{the line width for the confidence interval line segments}
+ \item{ci.lwd}{the line width for the confidence interval line
+ segments}
+ \item{ci.width}{length of lines used for the "t" at the end of confidence
+ interval line segments, as a multple of \code{width}. Defaults to 0.5.}
\item{plot.grid}{if \code{TRUE} a lined grid will be plotted behind the bars}
\item{grid.inc}{the number of grid increments to be plotted}
\item{grid.lty}{the line type for the grid}
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