Convert do.call calls to ParmOff

.gitignore

@@ -52,3 +52,4 @@ po/*~
 
 # RStudio Connect folder
 rsconnect/
+.positai

DESCRIPTION

@@ -1,13 +1,16 @@
 Package: magicaxis
 Type: Package
 Title: Pretty Scientific Plotting with Minor-Tick and Log Minor-Tick Support
-Version: 2.5.3
-Date: 2025-02-24
+Version: 2.6.0
+Date: 2026-05-14
 Authors@R: person(given = "Aaron",
                       family = "Robotham",
                       role = c("aut", "cre"),
                       email = "aaron.robotham@uwa.edu.au")
 Description: Functions to make useful (and pretty) plots for scientific plotting. Additional plotting features are added for base plotting, with particular emphasis on making attractive log axis plots.
 License: LGPL-3
-Suggests: imager, fst, plotly, abind
-Imports: grDevices, graphics, stats, celestial (>= 1.4.1), MASS, plotrix, sm, mapproj, RANN
+Suggests: imager, fst, plotly, abind, testthat (>= 3.0.0), knitr, rmarkdown
+Imports: grDevices, graphics, stats, celestial (>= 1.4.1), MASS, plotrix, sm, mapproj, RANN, ParmOff
+Remotes: asgr/ParmOff
+VignetteBuilder: knitr
+Config/testthat/edition: 3

NAMESPACE

@@ -7,11 +7,12 @@ import("mapproj")
 importFrom("grDevices", "hsv", "rainbow", "grey", "rgb", "dev.cur", "extendrange", "colorRampPalette", "hcl.colors", "grey.colors")
 importFrom("graphics", "arrows", "axis", "box", "contour", "image", "mtext", "par",
            "plot", "plot.new", "plot.window", "rect", "text", "abline", "layout",
-           "lines", "points", "polygon",  "hist")
+           "lines", "points", "points.default", "polygon",  "hist")
 importFrom("stats", "approxfun", "density", "median", "pnorm", "quantile", "sd", "rnorm", "ecdf", "qnorm", "mad", "aggregate", "runif")
 importFrom("celestial", "hms2deg", "dms2deg", "deg2hms", "deg2dms", "radec2xy", "xy2radec", "getpixscale")
 importFrom("RANN", "nn2")
 importFrom("plotrix", "color.legend", "draw.ellipse")
 importFrom("sm", "sm.density")
 importFrom("MASS", "kde2d")
 importFrom("utils", "str")
+importFrom("ParmOff", "ParmOff")

R/magaxis.R

@@ -5,15 +5,8 @@ function(side=1:2, majorn=5, minorn='auto', tcl=0.5, ratio=0.5, labels=TRUE, unl
          usepar=FALSE, grid=FALSE, grid.col='grey', grid.lty=1, grid.lwd=1, axis.lwd=1, 
          ticks.lwd=axis.lwd, axis.col='black', do.tick=TRUE, ...){
 dots=list(...)
-dotskeepaxis=c('cex.axis', 'col.axis', 'font.axis', 'xaxp', 'yaxp', 'tck', 'las', 'fg', 'xpd', 'xaxt', 'yaxt', 'col.ticks')
-dotskeepmtext=c('cex.lab', 'col.lab', 'font.lab')
-if(length(dots)>0){
-  dotsaxis=dots[names(dots) %in% dotskeepaxis]
-  dotsmtext=dots[names(dots) %in% dotskeepmtext]
-}else{
-  dotsaxis={}
-  dotsmtext={}
-}
+keepaxis = c('side', 'at', 'tcl', 'labels', 'tick', 'mgp', 'lwd', 'lwd.ticks', 'col', 'cex.axis', 'col.axis', 'font.axis', 'xaxp', 'yaxp', 'tck', 'las', 'fg', 'xpd', 'xaxt', 'yaxt', 'col.ticks')
+keepmtext = c('text', 'side', 'line', 'cex.lab', 'col.lab', 'font.lab')
 if(length(mtline)==1){mtline=rep(mtline,2)}
 majornlist=majorn
 minornlist=minorn
@@ -156,38 +149,35 @@ for(i in 1:length(side)){
     }
 
  		if(logged){
- 		  do.call("axis", c(list(side=currentside,at=powbase^major.ticks,tcl=tcl,labels=FALSE,tick=do.tick,mgp=mgp,lwd=axis.lwd,lwd.ticks=ticks.lwd,col=axis.col),dotsaxis))
+ 		  ParmOff(axis, c(list(side=currentside,at=powbase^major.ticks,tcl=tcl,labels=FALSE,tick=do.tick,mgp=mgp,lwd=axis.lwd,lwd.ticks=ticks.lwd,col=axis.col),dots), .use_args=keepaxis)
  		}else{
- 		  do.call("axis", c(list(side=currentside,at=major.ticks,tcl=tcl,labels=FALSE,tick=do.tick,mgp=mgp,lwd=axis.lwd,lwd.ticks=ticks.lwd,col=axis.col),dotsaxis))
+ 		  ParmOff(axis, c(list(side=currentside,at=major.ticks,tcl=tcl,labels=FALSE,tick=do.tick,mgp=mgp,lwd=axis.lwd,lwd.ticks=ticks.lwd,col=axis.col),dots), .use_args=keepaxis)
  		}
 
     if(labels){
       if(logged){
-        do.call("axis", c(list(side=currentside,at=powbase^labloc,tick=F,labels=uselabels,mgp=mgp,lwd=axis.lwd,lwd.ticks=ticks.lwd,col=axis.col),dotsaxis))
+        ParmOff(axis, c(list(side=currentside,at=powbase^labloc,tick=F,labels=uselabels,mgp=mgp,lwd=axis.lwd,lwd.ticks=ticks.lwd,col=axis.col),dots), .use_args=keepaxis)
       }else{
-        do.call("axis", c(list(side=currentside,at=labloc,tick=F,labels=uselabels,mgp=mgp,lwd=axis.lwd,lwd.ticks=ticks.lwd,col=axis.col),dotsaxis))
+        ParmOff(axis, c(list(side=currentside,at=labloc,tick=F,labels=uselabels,mgp=mgp,lwd=axis.lwd,lwd.ticks=ticks.lwd,col=axis.col),dots), .use_args=keepaxis)
       }
     }
 
     if(usemultloc==F & minorn>1){
       minors = minors[-c(1,length(minors))]
       minor.ticks = c(outer(minors, major.ticks, `+`))
       if(logged){
-        do.call("axis", c(list(side=currentside,at=powbase^minor.ticks,tcl=tcl*ratio,labels=FALSE,tick=do.tick,mgp=mgp,lwd=axis.lwd,lwd.ticks=ticks.lwd,col=axis.col),dotsaxis))
+        ParmOff(axis, c(list(side=currentside,at=powbase^minor.ticks,tcl=tcl*ratio,labels=FALSE,tick=do.tick,mgp=mgp,lwd=axis.lwd,lwd.ticks=ticks.lwd,col=axis.col), dots),.use_args=keepaxis)
       }else{
-        do.call("axis", c(list(side=currentside,at=minor.ticks,tcl=tcl*ratio,labels=FALSE,tick=do.tick,mgp=mgp,lwd=axis.lwd,lwd.ticks=ticks.lwd,col=axis.col),dotsaxis))
+        ParmOff(axis, c(list(side=currentside,at=minor.ticks,tcl=tcl*ratio,labels=FALSE,tick=do.tick,mgp=mgp,lwd=axis.lwd,lwd.ticks=ticks.lwd,col=axis.col),dots), .use_args=keepaxis)
       }
     }
   }
 
-  if(length(dotsmtext)>0){
-    names(dotsmtext)=c('cex', 'col', 'font')[match(names(dotsmtext), dotskeepmtext)]
-  }
   if(is.null(xlab)==FALSE){
-    do.call("mtext", c(list(text=xlab, side=ifelse(side[1] %in% c(1,3), side[1], side[2]), line=mtline[1]), dotsmtext))
+    ParmOff(mtext, c(list(text=xlab, side=ifelse(side[1] %in% c(1,3), side[1], side[2]), line=mtline[1]), dots), .use_args = keepmtext)
   }
   if(is.null(ylab)==FALSE){
-    do.call("mtext", c(list(text=ylab, side=ifelse(side[2] %in% c(2,4), side[2], side[1]), line=mtline[2]), dotsmtext))
+    ParmOff(mtext, c(list(text=ylab, side=ifelse(side[2] %in% c(2,4), side[2], side[1]), line=mtline[2]), dots), .use_args = keepmtext)
   }
 
 if(frame.plot){box()}

R/magbin.R

@@ -304,11 +304,11 @@ plot.magbin = function(x, colramp=hcl.colors(21), colstretch='lin', sizestretch=
   if(!is.na(x$dustlim)){
     x$bins = x$bins[x$bins[,'count']>x$dustlim,]
   }
-  colmap = do.call("magmap", c(list(data=x$bins[,colref], stretch=colstretch, range=c(1,length(colramp)), bad=NA), dotsmap))
+  colmap = ParmOff(magmap, c(list(data=x$bins[,colref], stretch=colstretch, range=c(1,length(colramp)), bad=NA), dotsmap))
   if(sizeref=='none'){
     sizemap = rep(1,dim(x$bins)[1])
   }else{
-    sizemap = do.call("magmap", c(list(data=x$bins[,sizeref], stretch=sizestretch, range=c(0,1), bad=NA)))$map
+    sizemap = ParmOff(magmap, c(list(data=x$bins[,sizeref], stretch=sizestretch, range=c(0,1), bad=NA)))$map
   }
   #colmap = magmap(x$bins[,3], stretch=stretch, bad=NA, range=c(1,length(colramp)))
   if('xlim' %in% names(dots)){
@@ -351,9 +351,9 @@ plot.magbin = function(x, colramp=hcl.colors(21), colstretch='lin', sizestretch=
 
       #4 (bottomright)
       par(mar=c(0,0,0,0))
-      do.call("magplot", c(list(NA, NA, xlim=xlim, ylim=ylim, side=c(1,2,3,4), labels=c(T,T,F,F)), dots))
+      ParmOff(magplot, c(list(NA, NA, xlim=xlim, ylim=ylim, side=c(1,2,3,4), labels=c(T,T,F,F)), dots))
     }else{
-      do.call("magplot", c(list(NA, NA, xlim=xlim, ylim=ylim), dots))
+      ParmOff(magplot, c(list(NA, NA, xlim=xlim, ylim=ylim), dots))
     }
   }
   #magplot(NA, NA, xlim=x$xlim, ylim=x$ylim, ...)
@@ -387,7 +387,7 @@ plot.magbin = function(x, colramp=hcl.colors(21), colstretch='lin', sizestretch=
       points(x$dust$x, x$dust$y, pch=pch.dust, col=colramp[1], cex=cex.dust)
     }else{
       if(colref=='zstat'){
-        colmapdust = do.call("magmap", c(list(data=x$dust$z, locut=colmap$datalim[1],
+        colmapdust = ParmOff(magmap, c(list(data=x$dust$z, locut=colmap$datalim[1],
                     hicut=colmap$datalim[2], type='num', stretch=colstretch,
                     range=c(1,length(colramp)), bad=NA)))$map
         points(x$dust$x, x$dust$y, pch=pch.dust, col=colramp[colmapdust], cex=cex.dust)
@@ -404,7 +404,7 @@ plot.magbin = function(x, colramp=hcl.colors(21), colstretch='lin', sizestretch=
         title = "norm"
       }
     }
-    do.call("magbar", c(list(range=colmap$datalim, log=colstretch=='log', col=colramp, title=title), dotsbar))
+    ParmOff(magbar, c(list(range=colmap$datalim, log=colstretch=='log', col=colramp, title=title), dotsbar))
   }
 }
 

R/magcon.R

@@ -42,7 +42,7 @@ function(x,y,h,doim=TRUE,docon=TRUE,dobar=TRUE,ngrid=100,add=FALSE,xlab='',ylab=
       usrlims=par()$usr
       rect(usrlims[1],usrlims[3],usrlims[2],usrlims[4],col=imcol[1])
     }
-    magimage(tempcon,col=imcol,axes=FALSE,add=TRUE,xlim=xlim,ylim=ylim,magmap=FALSE)
+    magimage(tempcon[c('x', 'y', 'z')],col=imcol,axes=FALSE,add=TRUE,xlim=xlim,ylim=ylim,magmap=FALSE)
   }
   if(doim & docon){contour(tempcon,levels=conlevels,add=TRUE,drawlabels=F,axes=FALSE,...)}
   if(doim==FALSE & docon){contour(tempcon,levels=conlevels,add=add,drawlabels=F,axes=FALSE,xlim=xlim,ylim=ylim,...);box()}

R/magimage.R

@@ -137,7 +137,7 @@ magimage = function(x, y, z, zlim, xlim, ylim, col = grey((0:1e3)/1e3), add = FA
     }
   }
 
-  do.call('image',c(list(x=x, y=y, z=z, zlim=zlim, xlim=xlim, ylim=ylim, col=col, add=add, useRaster=useRaster, axes=FALSE, asp=asp, xlab='', ylab='', main=''), dotsimage))
+  ParmOff(image,c(list(x=x, y=y, z=z, zlim=zlim, xlim=xlim, ylim=ylim, col=col, add=add, useRaster=useRaster, axes=FALSE, asp=asp, xlab='', ylab='', main=''), dotsimage))
 
   if(add==FALSE){
     if(axes){

R/magimageRGB.R

@@ -110,7 +110,7 @@ magimageRGB<-function(x, y, R, G, B, saturation=1, zlim, xlim, ylim, add = FALSE
   z = matrix(1:length(R),dim(R)[1])
   col = rgb(R,G,B)
 
-  do.call('image',c(list(x=x, y=y, z=z, zlim=zlim, xlim=xlim, ylim=ylim, col=col, add=add, useRaster=useRaster, axes=FALSE, asp=asp, xlab='', ylab='', main=''), dotsimage))
+  ParmOff(image,c(list(x=x, y=y, z=z, zlim=zlim, xlim=xlim, ylim=ylim, col=col, add=add, useRaster=useRaster, axes=FALSE, asp=asp, xlab='', ylab='', main=''), dotsimage))
   if(add==FALSE){
     if(axes){
       magaxis(...)

R/magplot.R

@@ -39,7 +39,7 @@ magplot =
            ...) {
     if (class(x)[1] == 'histogram') {
       dots = list(...)
-      do.call('maghist', c(
+      ParmOff(maghist, c(
         list(
           x = x,
           xlim = xlim,
@@ -121,8 +121,7 @@ magplot =
                 grid.lwd = grid.lwd,
                 axis.lwd = axis.lwd,
                 ticks.lwd = ticks.lwd,
-                axis.col = axis.col,
-                ...
+                axis.col = axis.col
               )
             },
             lwd = lwd,
@@ -220,8 +219,7 @@ magplot =
               grid.lwd = grid.lwd,
               axis.lwd = axis.lwd,
               ticks.lwd = ticks.lwd,
-              axis.col = axis.col,
-              ...
+              axis.col = axis.col
             )
           },
           lwd = lwd,
@@ -264,7 +262,7 @@ magplot =
             zstretch = 'log'
           }
         }
-        colmap = do.call("magmap", c(
+        colmap = ParmOff(magmap, c(
           list(
             data = z,
             stretch = zstretch,
@@ -317,11 +315,11 @@ magplot =
           xlim = xlim,
           ylim = ylim
         )
-        do.call("points", c(list(
+        ParmOff(points, c(list(
           x = x, y = y, col = zcol[colmap$map]
         ), dots))
         if (dobar) {
-          do.call("magbar", c(
+          ParmOff(magbar, c(
             list(
               range = colmap$datalim,
               log = zstretch == 'log',

R/magtri.R

@@ -8,6 +8,8 @@ magtri=function(chains, samples=1000, thin=1, samptype='end', grid=FALSE, do.tic
   }
   if(Npar<=1){stop('Need 2+ parameters!')}
 
+  dots=list(...)
+
   if(thin>1){
     chains=chains[seq(1,Nsamp,by=thin),,drop=FALSE]
     Nsamp=dim(chains)[1]
@@ -44,7 +46,7 @@ magtri=function(chains, samples=1000, thin=1, samptype='end', grid=FALSE, do.tic
         xtemp=chains[usesamps,i]
         if(sd(xtemp)==0){xtemp=xtemp+rnorm(samples,sd=1e-3)}
         plot(density(xtemp),axes=FALSE,main='',xlim=xrange)
-        magaxis(1,grid=grid, grid.col = 'lightgrey',labels=FALSE,do.tick=do.tick)
+        ParmOff(magaxis, dots, side=1, grid=grid, grid.col='lightgrey', labels=FALSE, do.tick=do.tick, .pass_dots=FALSE)
         abline(v=meanvec[i],lty=1,col='red')
         abline(v=meanvec[i]-sdvec[i],lty=3,col='red')
         abline(v=meanvec[i]+sdvec[i],lty=3,col='red')
@@ -55,14 +57,14 @@ magtri=function(chains, samples=1000, thin=1, samptype='end', grid=FALSE, do.tic
         if(i==1){
           plot.window(xlim=xrange,ylim=yrange)
           if(is.null(lab)){
-            magaxis(1,xlab=chaincolnames[i])
+            ParmOff(magaxis, dots, side=1, xlab=chaincolnames[i], .pass_dots=FALSE)
           }else{
-            magaxis(1,xlab=lab[[i]])
+            ParmOff(magaxis, dots, side=1, xlab=lab[[i]], .pass_dots=FALSE)
           }
           if(is.null(lab)){
-            magaxis(2,ylab=chaincolnames[j])
+            ParmOff(magaxis, dots, side=2, ylab=chaincolnames[j], .pass_dots=FALSE)
           }else{
-            magaxis(2,ylab=lab[[j]])
+            ParmOff(magaxis, dots, side=2, ylab=lab[[j]], .pass_dots=FALSE)
           }
         }
       }else{
@@ -73,9 +75,9 @@ magtri=function(chains, samples=1000, thin=1, samptype='end', grid=FALSE, do.tic
           ytemp=chains[usesamps,j]
           if(sd(xtemp)==0){xtemp=xtemp+rnorm(samples,sd=1e-3)}
           if(sd(ytemp)==0){ytemp=ytemp+rnorm(samples,sd=1e-3)}
-          magaxis(1:2,grid=grid, grid.col = 'lightgrey',labels=FALSE,do.tick=do.tick)
-          magcon(xtemp,ytemp,dobar=FALSE,doim=FALSE,add=TRUE,lty=c(2,1,3),xlim=xrange,ylim=yrange, h=c(diff(xrange),diff(yrange))/10, ...)
-          points(meanvec[i],meanvec[j],col='red',pch=4,cex=2)
+          ParmOff(magaxis, dots, side=1:2, grid=grid, grid.col='lightgrey', labels=FALSE, do.tick=do.tick, .pass_dots=FALSE)
+          ParmOff(magcon, dots, x=xtemp, y=ytemp, dobar=FALSE, doim=FALSE, add=TRUE, lty=c(2,1,3), xlim=xrange, ylim=yrange, h=c(diff(xrange),diff(yrange))/10, .pass_dots=FALSE)
+          ParmOff(points, dots, x=meanvec[i], y=meanvec[j], col='red', pch=4, cex=2, .pass_dots=FALSE)
           box()
           abline(v=meanvec[i],lty=1,col='red')
           abline(v=meanvec[i]-sdvec[i],lty=3,col='red')
@@ -85,23 +87,23 @@ magtri=function(chains, samples=1000, thin=1, samptype='end', grid=FALSE, do.tic
           }
           if(j==1){
             if(is.null(lab)){
-              magaxis(1,xlab=chaincolnames[i])
+              ParmOff(magaxis, dots, side=1, xlab=chaincolnames[i], .pass_dots=FALSE)
             }else{
-              magaxis(1,xlab=lab[[i]])
+              ParmOff(magaxis, dots, side=1, xlab=lab[[i]], .pass_dots=FALSE)
             }
           }
         }else{
           plot.new()
           plot.window(xlim=xrange,ylim=yrange)
-          magaxis(1:2,grid=grid, grid.col = 'lightgrey',labels=FALSE,do.tick=do.tick)
-          points(chains[usesamps,c(i,j)],pch='.',col='darkgrey')
-          points(meanvec[i],meanvec[j],col='red',pch=4,cex=2)
+          dots_carry = ParmOff(magaxis, dots, side=1:2, grid=grid, grid.col='lightgrey', labels=FALSE, do.tick=do.tick, .pass_dots=FALSE, .return='func_args')$args_out$ignore_args
+          ParmOff(points.default, dots_carry, x=chains[usesamps,i], y=chains[usesamps,j], pch='.', col='darkgrey', .pass_dots=TRUE)
+          ParmOff(points.default, dots_carry, x=meanvec[i], y=meanvec[j], col='red', pch=4, cex=2, .pass_dots=TRUE)
           box()
           if(i==1){
             if(is.null(lab)){
-              magaxis(2,ylab=chaincolnames[j])
+              ParmOff(magaxis, dots, side=2, ylab=chaincolnames[j], .pass_dots=FALSE)
             }else{
-              magaxis(2,ylab=lab[[j]])
+              ParmOff(magaxis, dots, side=2, ylab=lab[[j]], .pass_dots=FALSE)
             }
           }
         }

man/magaxis.Rd

@@ -129,7 +129,6 @@ magaxis(side=c(1,3),unlog=c(TRUE,FALSE))
 
 plot(x,y,axes=FALSE,log='x')
 magaxis()
-
 }
 
 % Add one or more standard keywords, see file 'KEYWORDS' in the

man/magmap.Rd

@@ -131,7 +131,6 @@ stretch='asinh')$map
 magplot(datastretch[,1],datastretch[,3],side=1)
 axis(2,asinhticks,labels=c(-10^(4:0),0,10^(0:4)))
 abline(h=magmap(0,lo=-1e4,hi=1e4,range=c(0,1),type='num',stretch='asinh')$map)
-
 }
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(magicaxis)
+
+test_check("magicaxis")