[CHNOSZ-commits] r296 - in pkg/CHNOSZ: . R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Dec 5 04:18:54 CET 2017
Author: jedick
Date: 2017-12-05 04:18:53 +0100 (Tue, 05 Dec 2017)
New Revision: 296
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/diagram.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/diagram.Rd
Log:
diagram(): add srt argument
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-11-21 15:16:10 UTC (rev 295)
+++ pkg/CHNOSZ/DESCRIPTION 2017-12-05 03:18:53 UTC (rev 296)
@@ -1,6 +1,6 @@
-Date: 2017-11-21
+Date: 2017-12-05
Package: CHNOSZ
-Version: 1.1.3-2
+Version: 1.1.3-3
Title: Thermodynamic Calculations for Geobiochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R 2017-11-21 15:16:10 UTC (rev 295)
+++ pkg/CHNOSZ/R/diagram.R 2017-12-05 03:18:53 UTC (rev 296)
@@ -12,14 +12,14 @@
#source("util.misc.R")
diagram <- function(
- # primary input
+ # species affinities or activities
eout,
# what to plot
what="loga.equil", alpha=FALSE, normalize=FALSE, as.residue=FALSE, balance=NULL,
groups=as.list(1:length(eout$values)), xrange=NULL,
- # plot dimensions
+ # figure size and sides for axis tick marks
mar=NULL, yline=par("mgp")[1]+0.3, side=1:4,
- # axes
+ # axis limits and labels
ylog=TRUE, xlim=NULL, ylim=NULL, xlab=NULL, ylab=NULL,
# sizes
cex=par("cex"), cex.names=1, cex.axis=par("cex"),
@@ -28,8 +28,10 @@
# colors
col=par("col"), col.names=par("col"), fill=NULL,
fill.NA="slategray1", limit.water=TRUE,
- # labels
- names=NULL, main=NULL, legend.x=NA, format.names=TRUE, adj=0.5, dy=0,
+ # field and line labels
+ names=NULL, format.names=TRUE, adj=0.5, dy=0, srt=0,
+ # title and legend
+ main=NULL, legend.x=NA,
# plotting controls
add=FALSE, plot.it=TRUE, tplot=TRUE, ...
) {
@@ -295,6 +297,7 @@
if(is.na(legend.x)) {
maxvals <- do.call(pmax, pv)
dy <- rep(dy, length.out=length(plotvals))
+ srt <- rep(srt, length.out=length(plotvals))
# don't assign to adj becuase that messes up the missing test below
alladj <- rep(adj, length.out=length(plotvals))
for(i in 1:length(plotvals)) {
@@ -326,7 +329,8 @@
}
}
# also include y-offset (dy) and y-adjustment (labels bottom-aligned with the line)
- text(xvalues[imax], plotvals[[i]][imax] + dy[i], labels=names[i], adj=c(thisadj, 0), cex=cex.names)
+ # .. and srt (string rotation) 20171127
+ text(xvalues[imax], plotvals[[i]][imax] + dy[i], labels=names[i], adj=c(thisadj, 0), cex=cex.names, srt=srt[i])
}
} else legend(x=legend.x, lty=lty, legend=names, col=col, cex=cex.names, lwd=lwd, ...)
}
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-11-21 15:16:10 UTC (rev 295)
+++ pkg/CHNOSZ/inst/NEWS 2017-12-05 03:18:53 UTC (rev 296)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-2 (2017-11-21)
+CHANGES IN CHNOSZ 1.1.3-3 (2017-12-05)
--------------------------------------
- Lines in 1-D diagram()s can optionally be drawn as splines using the
@@ -8,6 +8,8 @@
- Add dumpdata() for returning/writing all packaged data (including
default database and optional data files).
+- Add 'srt' argument to diagram() (rotation of line labels).
+
CHANGES IN CHNOSZ 1.1.3 (2017-11-13)
------------------------------------
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2017-11-21 15:16:10 UTC (rev 295)
+++ pkg/CHNOSZ/man/diagram.Rd 2017-12-05 03:18:53 UTC (rev 296)
@@ -9,15 +9,28 @@
}
\usage{
- diagram(eout, what = "loga.equil", alpha = FALSE, normalize = FALSE,
+ diagram(
+ # species affinities or activities
+ eout,
+ # what to plot
+ what = "loga.equil", alpha = FALSE, normalize = FALSE,
as.residue = FALSE, balance=NULL, groups=as.list(1:length(eout$values)),
+ # figure size and sides for axis tick marks
xrange=NULL, mar=NULL, yline=par("mgp")[1]+0.3, side=1:4,
+ # axis limits and labels
ylog=TRUE, xlim=NULL, ylim=NULL, xlab=NULL, ylab=NULL,
+ # character sizes
cex=par("cex"), cex.names=1, cex.axis=par("cex"),
+ # line styles
lty=NULL, lwd=par("lwd"), dotted=NULL, spline.method = NULL,
+ # colors
col=par("col"), col.names=par("col"), fill=NULL,
fill.NA="slategray1", limit.water=TRUE,
- names=NULL, main=NULL, legend.x=NA, format.names=TRUE, adj=0.5, dy=0,
+ # field and line labels
+ names=NULL, format.names=TRUE, adj=0.5, dy=0, srt=0,
+ # title and legend
+ main=NULL, legend.x=NA,
+ # plotting controls
add=FALSE, plot.it=TRUE, tplot=TRUE, ...)
strip(affinity, ispecies = NULL, col = NULL, ns = NULL,
xticks = NULL, ymin = -0.2, xpad = 1, cex.names = 0.7)
@@ -54,11 +67,12 @@
\item{fill.NA}{character, color for grid points with NA values}
\item{limit.water}{logical, set NA values beyond water stability limits?}
\item{names}{character, names of species for activity lines or predominance fields}
- \item{main}{character, a main \code{\link{title}} for the plot; \code{NULL} means to plot no title}
- \item{legend.x}{character, description of legend placement passed to \code{\link{legend}}}
\item{format.names}{logical, apply formatting to chemical formulas?}
\item{adj}{numeric, adjustment for line labels}
\item{dy}{numeric, y offset for line labels}
+ \item{srt}{numeric, rotation for line labels}
+ \item{main}{character, a main \code{\link{title}} for the plot; \code{NULL} means to plot no title}
+ \item{legend.x}{character, description of legend placement passed to \code{\link{legend}}}
\item{add}{logical, add to current plot?}
\item{plot.it}{logical, make a plot?}
\item{tplot}{logical, set up plot with \code{\link{thermo.plot.new}}?}
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