R/plotMap.CSV.R
In wStockhausen/wtsGMT: Functions for creating maps with GMT 4.5 (and maybe 5.1)
Defines functions
plotMap.CSV
Documented in
plotMap.CSV
#'
#'@title Plots a dataframe or csv file on a map using GMT.
#'
#'@description A function to plot a dataframe or csv file on a map using GMT.
#'
#'@details
#' External Requirements:
#' * GMT 4.5.x
#' * on Windows, need both gswin32c and gswin64c installed
#' * on network, need to use mapped drives to specify files
#'\cr
#'Z-values > zscl are truncated to zscl so they will plot (otherwise GMT removes them completely, apparently)
#'
#' @param dfr = dataframe or csv file to plot
#' @param lat = column name containing latitudes
#' @param lon = column name containing longitudes
#' @param col = name of column containing z data
#' @param gmt = GMT version (4 or 5)
#' @param title = map title
#' @param year = year label
#' @param xyrng = x-y range for map as GMT string ('xmin/xmax/ymin/ymax')
#' @param zscl = z-scale (max) for map
#' @param zlab = label for z axes
#' @param zunits = units for z axes
#' @param rotate = flag (T/F) or value of angle for map rotation (angle=180 if rotate=T/F)
#' @param elev = elevation for map perspective is rotate is not FALSE
#' @param delx = x increment for associated grids
#' @param dely = y increment for associated grids
#' @param logtr = flag to ln-transform z data
#' @param blocktype = flag ('MEAN' or 'SUM') for grouping data
#' @param plt_blocktype = flag ('SMOOTH','COARSE') for displaying surface
#' @param plt_blocklocations = flag to plot block locations as X's
#' @param plt_surface = flag to plot data as a color density image
#' @param plt_bars = flag to plot data as bars
#' @param plt_colorscale = flag to plot color scale
#' @param plt_reflines = flag to include refernce lines on map
#' @param reflines = list of lists(lon=,lat=) of reference lines to plot
#' @param plt_title = flag to include title on map
#' @param psFile = filename for output file (no extension--will be pdf)
#' @param pdfDir = directory for output file
#' @param bathymetryfile = filename of bathymetry to plot
#' @param cleanup = flag to remove temporary files
#'
#' @return z-scale used for plot.
#'
#'@importFrom wtsUtilities computeTickInterval
#'@importFrom wtsUtilities getOperatingSystem
#'@importFrom wtsUtilities getCSV
#'
#' @export
#'
plotMap.CSV<-function(dfr=NULL,
lat='latitude',
lon='longitude',
col=NULL,
gmt=4,
title='Tanner Crab',
year='',
xyrng='180/205/54/62',
zscl=NULL,
zlab='Catch',
zunits='num. crab',
rotate=FALSE,
elev=70,
delx=0.5,
dely=0.25,
blocktype=c('MEAN','SUM'),
plt_blocktype=c('SMOOTH','COARSE'),
logtr=FALSE,
plt_title=FALSE,
plt_bars=FALSE,
plt_surface=FALSE,
plt_blocklocations=FALSE,
plt_colorscale=plt_surface|plt_bars,
plt_stations=FALSE,
plt_reflines=FALSE,
reflines=list(list(lon=-166+0*seq(from=50,to=80,by=1),lat=seq(from=50,to=80,by=1))),
psFile='catchMaps',
toPDF=FALSE,
bathymetryFile=file.path(getwd(),'data/depthcontour_200500.prn'),
cleanup=FALSE
) {
#check the operating platform
MacOSX<-'MacOSX';
Windws<-'Windows';
platform<-getOperatingSystem();
#check for unc paths
if (platform==Windws){
if (length(grep('\\\\',getwd()))>0){
cat("Working dir is using a network path:\n",
getwd(),'\n',
'This function uses Windows .bat files.\n',
'Please use a mapped drive path for the working directory!!\n',
'Exiting function\n');
return;
}
}
#read in dataframe, if necessary
retDFR<-FALSE;
if (!is.data.frame(dfr)){
#read in table from csv file
if (is.null(dfr)) {
dfr = getCSV(caption="Select csv file to plot");
if (is.null(dfr)) return(NULL);
} else {
dfr<-read.csv(dfr,stringsAsFactors=FALSE);
}
retDFR<-TRUE;
names(dfr)<-tolower(names(dfr));
}
#extract relevant columns, convert lon's to 0-360
dfr1<-data.frame(lon=dfr[[lon]],lat=dfr[[lat]]);
dfr1[["lon"]]<-dfr1[["lon"]]*(dfr1[["lon"]]>0) + (360+dfr1[["lon"]])*(dfr1[["lon"]]<0);
dfr1[["z1"]] <-dfr[[col]];
if (plt_surface){
#create grid
dfr1p<-gridCSV(dfr1,lat='lat',lon='lon',col='z1',logtr=logtr,
xyrng=xyrng,delx=delx,dely=dely,
blocktype=blocktype);
if (logtr) dfr1p$z1<-(10^dfr1p$z1)-1;#transform back
}
#calculate z-scaling information
if (is.null(zscl)) {
vls<-dfr1$z1;
if (plt_surface) vls<-c(vls,dfr1p$z1);
zscl<-calcZScale(vls,logtr=logtr);#z-scale in (possibly transformed) data units
}
#z values > zscl appear to be removed in GMT (not even just clipped), so
#need to truncate values to zscl
if (logtr){
idx<-(log(dfr1$z1+1)/log(10)<=zscl)
dfr1$z1<-log(dfr1$z1+1)/log(10)*idx+zscl(!idx);#z log10 transformed (not ln)
zscale<-zscl;
zunits<-paste('log@-10@-(',zunits,'+1)',sep='');
} else {
idx<-(dfr1$z1<=zscl)
dfr1$z1<-dfr1$z1*idx+zscl*(!idx)
z10<-floor(log(zscl)/log(10)); #z-scale normalization factor for factor of 10 scaling
zscale<-zscl/(10^z10); #z-scale normalized by factor for factor of 10 scaling
dfr1$z1<-dfr1$z1/(10^z10);#z normalized by factor for factor of 10 scaling
zunits<-paste('10@+',z10,'@+ ',zunits,sep='');
}
dfr1[["z2"]]<-dfr1[["z1"]];
#z axis information
zinc <-zscale/100; #increment for color scale
zstride1<-computeTickInterval(zscale,1); #major tick interval
zstride2<-zstride1/5; #minor tick interval
xyzfile<-file.path(getwd(),'tmp_xyzvals.txt');
write.table(dfr1,
xyzfile,
sep=' ',
na="",
quote=FALSE,
col.names=FALSE,
row.names=FALSE)
if (plt_reflines){
str<-'';
for (refline in reflines){
str<-paste(str,">\n",sep='');
lons<-refline$lon*(refline$lon>=0) + (360+refline$lon)*(refline$lon<0);
lons<-refline$lon;
lats<-refline$lat;
for (i in 1:length(lons)){
str<-paste(str,' ',lons[i],' ',lats[i],' 0.0 ',"\n",sep='');
}
}
cat(str,file=file.path(getwd(),'reflines.txt'));
}
yearlabel<-paste(year,sep='');
psf<-paste(psFile,'.ps',sep='');
if (file.exists(psf)){
cat("Deleting old version of '",psf,"'.\n",sep='')
file.remove(psf);
}
blktyp<-'';
if (blocktype[1]=='SUM') blktyp='-Sz';
if (platform==MacOSX){shll<-'#!/bin/bash +'; batfile<-'plotMap.sh'; set<-'export ';}
if (platform==Windws){shll<-''; batfile<-'plotMap.bat'; set<-'set ';}
setenvs<-paste("#--ENVIRONMENT VARIABLES\n",
set, 'delx=',delx,'\n',
set, 'dely=',dely,'\n',
set, 'zlab="',zlab,'"\n',
set, 'zscale=',zscale,'\n',
set, 'zinc=',zinc,'\n',
set, 'zstride1=',zstride1,'\n',
set, 'zstride2=',zstride2,'\n',
set, 'zunits="',zunits,'"\n',
set, 'title="',title,'"\n',
set, 'yearlabel="',yearlabel,'"',
sep='');
rngxy<-paste("-R",xyrng,sep='');
rngxyz<-rngxy;
ymx<-3.65;
axs<-"WESn";
JZ<-'';
rot3d<-'';
if (is.logical(rotate)&&(!rotate)) {
plt_bars<-FALSE;#can't plot bars because elevation is effectively 90
} else {
if (is.logical(rotate)) {rotate<-180;} #rotate was TRUE, so set to 180
rngxyz<-paste(rngxy,'/0/',zscale,sep='');
ymx<-3.65;
axs<-"wESn";
if (gmt==4){
rot3d<-paste('-E',rotate,'/',elev,sep='');
} else {
JZ<-paste('-JZ',ymx,sep='');
rot3d<-paste('-p',rotate,'/',elev,'/0',sep='');
}
}
cat("rotate =",rotate,"\n");
cat("rot3d =",rot3d,'\n');
setenvs<-paste(setenvs,"\n",
set,"rngxy='",rngxy,"'\n",
set,"rngxyz='",rngxyz,"'\n",
set,"rot3d='",rot3d,"'\n",
set,"JZ='",JZ,"'\n",
set,"ymx=",ymx,"\n",
set,"axs=",axs,
sep='')
delxy<-paste(delx,"/",dely,sep='');
setenvs<-paste(setenvs,"\n",
set,"delxy=",delxy,"\n",
set,"mapbndry=-Bpa5f1g1.0/a5f1g1.0",axs,"\n",
set,"geotransform=-JB192.5/58/50/65/5.5i\n",
set,'yearlabelinfo="181 55.5 16 0 4 BL ',yearlabel,'"\n',
set,"mapscl=-L182/55/55/100k\n",
set,"xyblksz=-I",delxy,"\n",
set,"blocktype=",blktyp,"\n",
set,"xs=1i\n",
set,"ys=1i",
sep='')
#set values for input file and output postscript file
setenvs<-paste(setenvs,"\n","#--IMPORTANT FILES",sep='\n')
setenvs<-paste(setenvs,"\n",set,"infile='",xyzfile,"'\n",sep='')
setenvs<-paste(setenvs,"\n",set,"postfile='",psf,"'\n",sep='')
setenvs<-paste(setenvs,"\n",set,"bathymetryfile='",bathymetryFile,"'\n",sep='')
cat("setenvs = ",setenvs,sep='\n')
if (gmt==4) {
script<-createPlotScript.GMT4(delx=delx,
dely=dely,
logtr=logtr,
blocktype=blocktype[1],
plt_blocktype=plt_blocktype[1],
plt_surface=plt_surface,
plt_bars=plt_bars,
plt_blocklocations=plt_blocklocations,
plt_stations=plt_stations,
plt_colorscale=plt_colorscale,
plt_reflines=plt_reflines,
plt_title=plt_title,
cleanup=cleanup);
}
cat("script = ",script,sep='\n');
cat(shll,'\n',
setenvs,'\n',
script,
file=batfile,sep='');
# readline(prompt='start runGMT >');
# if (platform==MacOSX) Sys.chmod(batfile);#make it executable
cat("Starting GMT\n")
if (platform==MacOSX) system(paste('/bin/bash ',batfile,sep=''));
if (platform==Windws) system(batfile,show.output.on.console=TRUE);
if (cleanup) {
file.remove(xyzfile);
file.remove(batfile);
}
cat("Finished running GMT portion\n");
if (toPDF){
createPDF.fromPS(psFile,psFiles=paste0(psFile,".ps"));
}
cat('\nzscale used for plots was ',zscl,'\n\n\n');
if (retDFR) return(invisible(list(dfr=dfr,zscl=zscl)));
return(invisible(zscl));
}
wStockhausen/wtsGMT documentation built on May 3, 2019, 7:36 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions plotMap.CSV
Documented in plotMap.CSV
#'
#'@title Plots a dataframe or csv file on a map using GMT.
#'
#'@description A function to plot a dataframe or csv file on a map using GMT.
#'
#'@details
#' External Requirements:
#' * GMT 4.5.x
#' * on Windows, need both gswin32c and gswin64c installed
#' * on network, need to use mapped drives to specify files
#'\cr
#'Z-values > zscl are truncated to zscl so they will plot (otherwise GMT removes them completely, apparently)
#'
#' @param dfr = dataframe or csv file to plot
#' @param lat = column name containing latitudes
#' @param lon = column name containing longitudes
#' @param col = name of column containing z data
#' @param gmt = GMT version (4 or 5)
#' @param title = map title
#' @param year = year label
#' @param xyrng = x-y range for map as GMT string ('xmin/xmax/ymin/ymax')
#' @param zscl = z-scale (max) for map
#' @param zlab = label for z axes
#' @param zunits = units for z axes
#' @param rotate = flag (T/F) or value of angle for map rotation (angle=180 if rotate=T/F)
#' @param elev = elevation for map perspective is rotate is not FALSE
#' @param delx = x increment for associated grids
#' @param dely = y increment for associated grids
#' @param logtr = flag to ln-transform z data
#' @param blocktype = flag ('MEAN' or 'SUM') for grouping data
#' @param plt_blocktype = flag ('SMOOTH','COARSE') for displaying surface
#' @param plt_blocklocations = flag to plot block locations as X's
#' @param plt_surface = flag to plot data as a color density image
#' @param plt_bars = flag to plot data as bars
#' @param plt_colorscale = flag to plot color scale
#' @param plt_reflines = flag to include refernce lines on map
#' @param reflines = list of lists(lon=,lat=) of reference lines to plot
#' @param plt_title = flag to include title on map
#' @param psFile = filename for output file (no extension--will be pdf)
#' @param pdfDir = directory for output file
#' @param bathymetryfile = filename of bathymetry to plot
#' @param cleanup = flag to remove temporary files
#'
#' @return z-scale used for plot.
#'
#'@importFrom wtsUtilities computeTickInterval
#'@importFrom wtsUtilities getOperatingSystem
#'@importFrom wtsUtilities getCSV
#'
#' @export
#'
plotMap.CSV<-function(dfr=NULL,
lat='latitude',
lon='longitude',
col=NULL,
gmt=4,
title='Tanner Crab',
year='',
xyrng='180/205/54/62',
zscl=NULL,
zlab='Catch',
zunits='num. crab',
rotate=FALSE,
elev=70,
delx=0.5,
dely=0.25,
blocktype=c('MEAN','SUM'),
plt_blocktype=c('SMOOTH','COARSE'),
logtr=FALSE,
plt_title=FALSE,
plt_bars=FALSE,
plt_surface=FALSE,
plt_blocklocations=FALSE,
plt_colorscale=plt_surface|plt_bars,
plt_stations=FALSE,
plt_reflines=FALSE,
reflines=list(list(lon=-166+0*seq(from=50,to=80,by=1),lat=seq(from=50,to=80,by=1))),
psFile='catchMaps',
toPDF=FALSE,
bathymetryFile=file.path(getwd(),'data/depthcontour_200500.prn'),
cleanup=FALSE
) {
#check the operating platform
MacOSX<-'MacOSX';
Windws<-'Windows';
platform<-getOperatingSystem();
#check for unc paths
if (platform==Windws){
if (length(grep('\\\\',getwd()))>0){
cat("Working dir is using a network path:\n",
getwd(),'\n',
'This function uses Windows .bat files.\n',
'Please use a mapped drive path for the working directory!!\n',
'Exiting function\n');
return;
}
}
#read in dataframe, if necessary
retDFR<-FALSE;
if (!is.data.frame(dfr)){
#read in table from csv file
if (is.null(dfr)) {
dfr = getCSV(caption="Select csv file to plot");
if (is.null(dfr)) return(NULL);
} else {
dfr<-read.csv(dfr,stringsAsFactors=FALSE);
}
retDFR<-TRUE;
names(dfr)<-tolower(names(dfr));
}
#extract relevant columns, convert lon's to 0-360
dfr1<-data.frame(lon=dfr[[lon]],lat=dfr[[lat]]);
dfr1[["lon"]]<-dfr1[["lon"]]*(dfr1[["lon"]]>0) + (360+dfr1[["lon"]])*(dfr1[["lon"]]<0);
dfr1[["z1"]] <-dfr[[col]];
if (plt_surface){
#create grid
dfr1p<-gridCSV(dfr1,lat='lat',lon='lon',col='z1',logtr=logtr,
xyrng=xyrng,delx=delx,dely=dely,
blocktype=blocktype);
if (logtr) dfr1p$z1<-(10^dfr1p$z1)-1;#transform back
}
#calculate z-scaling information
if (is.null(zscl)) {
vls<-dfr1$z1;
if (plt_surface) vls<-c(vls,dfr1p$z1);
zscl<-calcZScale(vls,logtr=logtr);#z-scale in (possibly transformed) data units
}
#z values > zscl appear to be removed in GMT (not even just clipped), so
#need to truncate values to zscl
if (logtr){
idx<-(log(dfr1$z1+1)/log(10)<=zscl)
dfr1$z1<-log(dfr1$z1+1)/log(10)*idx+zscl(!idx);#z log10 transformed (not ln)
zscale<-zscl;
zunits<-paste('log@-10@-(',zunits,'+1)',sep='');
} else {
idx<-(dfr1$z1<=zscl)
dfr1$z1<-dfr1$z1*idx+zscl*(!idx)
z10<-floor(log(zscl)/log(10)); #z-scale normalization factor for factor of 10 scaling
zscale<-zscl/(10^z10); #z-scale normalized by factor for factor of 10 scaling
dfr1$z1<-dfr1$z1/(10^z10);#z normalized by factor for factor of 10 scaling
zunits<-paste('10@+',z10,'@+ ',zunits,sep='');
}
dfr1[["z2"]]<-dfr1[["z1"]];
#z axis information
zinc <-zscale/100; #increment for color scale
zstride1<-computeTickInterval(zscale,1); #major tick interval
zstride2<-zstride1/5; #minor tick interval
xyzfile<-file.path(getwd(),'tmp_xyzvals.txt');
write.table(dfr1,
xyzfile,
sep=' ',
na="",
quote=FALSE,
col.names=FALSE,
row.names=FALSE)
if (plt_reflines){
str<-'';
for (refline in reflines){
str<-paste(str,">\n",sep='');
lons<-refline$lon*(refline$lon>=0) + (360+refline$lon)*(refline$lon<0);
lons<-refline$lon;
lats<-refline$lat;
for (i in 1:length(lons)){
str<-paste(str,' ',lons[i],' ',lats[i],' 0.0 ',"\n",sep='');
}
}
cat(str,file=file.path(getwd(),'reflines.txt'));
}
yearlabel<-paste(year,sep='');
psf<-paste(psFile,'.ps',sep='');
if (file.exists(psf)){
cat("Deleting old version of '",psf,"'.\n",sep='')
file.remove(psf);
}
blktyp<-'';
if (blocktype[1]=='SUM') blktyp='-Sz';
if (platform==MacOSX){shll<-'#!/bin/bash +'; batfile<-'plotMap.sh'; set<-'export ';}
if (platform==Windws){shll<-''; batfile<-'plotMap.bat'; set<-'set ';}
setenvs<-paste("#--ENVIRONMENT VARIABLES\n",
set, 'delx=',delx,'\n',
set, 'dely=',dely,'\n',
set, 'zlab="',zlab,'"\n',
set, 'zscale=',zscale,'\n',
set, 'zinc=',zinc,'\n',
set, 'zstride1=',zstride1,'\n',
set, 'zstride2=',zstride2,'\n',
set, 'zunits="',zunits,'"\n',
set, 'title="',title,'"\n',
set, 'yearlabel="',yearlabel,'"',
sep='');
rngxy<-paste("-R",xyrng,sep='');
rngxyz<-rngxy;
ymx<-3.65;
axs<-"WESn";
JZ<-'';
rot3d<-'';
if (is.logical(rotate)&&(!rotate)) {
plt_bars<-FALSE;#can't plot bars because elevation is effectively 90
} else {
if (is.logical(rotate)) {rotate<-180;} #rotate was TRUE, so set to 180
rngxyz<-paste(rngxy,'/0/',zscale,sep='');
ymx<-3.65;
axs<-"wESn";
if (gmt==4){
rot3d<-paste('-E',rotate,'/',elev,sep='');
} else {
JZ<-paste('-JZ',ymx,sep='');
rot3d<-paste('-p',rotate,'/',elev,'/0',sep='');
}
}
cat("rotate =",rotate,"\n");
cat("rot3d =",rot3d,'\n');
setenvs<-paste(setenvs,"\n",
set,"rngxy='",rngxy,"'\n",
set,"rngxyz='",rngxyz,"'\n",
set,"rot3d='",rot3d,"'\n",
set,"JZ='",JZ,"'\n",
set,"ymx=",ymx,"\n",
set,"axs=",axs,
sep='')
delxy<-paste(delx,"/",dely,sep='');
setenvs<-paste(setenvs,"\n",
set,"delxy=",delxy,"\n",
set,"mapbndry=-Bpa5f1g1.0/a5f1g1.0",axs,"\n",
set,"geotransform=-JB192.5/58/50/65/5.5i\n",
set,'yearlabelinfo="181 55.5 16 0 4 BL ',yearlabel,'"\n',
set,"mapscl=-L182/55/55/100k\n",
set,"xyblksz=-I",delxy,"\n",
set,"blocktype=",blktyp,"\n",
set,"xs=1i\n",
set,"ys=1i",
sep='')
#set values for input file and output postscript file
setenvs<-paste(setenvs,"\n","#--IMPORTANT FILES",sep='\n')
setenvs<-paste(setenvs,"\n",set,"infile='",xyzfile,"'\n",sep='')
setenvs<-paste(setenvs,"\n",set,"postfile='",psf,"'\n",sep='')
setenvs<-paste(setenvs,"\n",set,"bathymetryfile='",bathymetryFile,"'\n",sep='')
cat("setenvs = ",setenvs,sep='\n')
if (gmt==4) {
script<-createPlotScript.GMT4(delx=delx,
dely=dely,
logtr=logtr,
blocktype=blocktype[1],
plt_blocktype=plt_blocktype[1],
plt_surface=plt_surface,
plt_bars=plt_bars,
plt_blocklocations=plt_blocklocations,
plt_stations=plt_stations,
plt_colorscale=plt_colorscale,
plt_reflines=plt_reflines,
plt_title=plt_title,
cleanup=cleanup);
}
cat("script = ",script,sep='\n');
cat(shll,'\n',
setenvs,'\n',
script,
file=batfile,sep='');
# readline(prompt='start runGMT >');
# if (platform==MacOSX) Sys.chmod(batfile);#make it executable
cat("Starting GMT\n")
if (platform==MacOSX) system(paste('/bin/bash ',batfile,sep=''));
if (platform==Windws) system(batfile,show.output.on.console=TRUE);
if (cleanup) {
file.remove(xyzfile);
file.remove(batfile);
}
cat("Finished running GMT portion\n");
if (toPDF){
createPDF.fromPS(psFile,psFiles=paste0(psFile,".ps"));
}
cat('\nzscale used for plots was ',zscl,'\n\n\n');
if (retDFR) return(invisible(list(dfr=dfr,zscl=zscl)));
return(invisible(zscl));
}
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