# Plotting spatial data Plots spatial data (e.g. 2D oceanographic data). Valid input data are objects of class 'Raster' ('RasterLayer', 'RasterStack' or 'RasterBrick'), 'ncdf4' (already loaded netcdf files) or a character strings indicating `'bathy'`metric data, 'gz'- or '.nc-files' (netcdf). See also name_split for further information on `'.gz'`-file nomenclature. ```r ## S4 method for signature 'bathy' v(obj, v_area, lon, lat, resolution=4, keep=F, savename.bathy, folder.bathy=".", adaptive.vals=T, cb.title, show.colorbar=T,...) ## S4 method for signature 'nc' v(obj, varname, t=1, layer=t, adaptive.vals=T, dates, cb.xlab=varname, show.colorbar=T ,...) ## S4 method for signature 'ncdf4' v(obj, varname, t=1, layer=t, adaptive.vals=T, dates, cb.xlab=varname, show.colorbar=T, ...) ## S4 method for signature 'RasterLayer' v(obj, varname, t=1, layer=t, ...) ## S4 method for signature 'RasterBrick' v(obj, varname, t=1, layer=t, ...) ## S4 method for signature 'RasterStack' v(obj, varname, t=1, layer=t, ...) ## S4 method for signature 'gz' v(obj, v_area, adaptive.vals=F, show.colorbar=T,...) ``` ## Arguments - `obj`: object of class 'Raster' ('RasterLayer', 'RasterStack' or 'RasterBrick'), '`ncdf4`' or a character string indicating , `'bathy'`metric data, `'.gz'`- or `'.nc'`-files to plot. - `v_area`: character string identifying the region that should be plotted, or in case of `obj == 'bathy'`, also a Raster* or Extent object. If missing, region is derived from the `'.gz'`-filename. See region_definitions for area definitions and use add.region to add new regions. - `adaptive.vals`: sets minimum and maximum z-value according to the `'.gz'`-files value range. (ATTENTION! `minv` and `maxv` are disregarded if set!). (default is `TRUE` for non-`'.gz'`-files. If `FALSE` or not set, default value from the parameter_definitions -dataset will be applied according to the `param`-value. - `t, layer`: layer/time stemp to select in multi-layer files/objects (e.g. ncdf4, RasterStack). - `dates`: vector of type 'character' indicating dates per layer, used to define the title of the colorbar. Argument is omitted for `'.gz'`-files but date-information is derived from the filename. For `'.nc'`-files or 'ncdf4'-objects, date information is derived from the time-vector. For raster -objects the layer name is applied. - `varname`: character string indicating the name of the variable to plot. For `'.nc'`-files or 'ncdf4'-objects, this name must correspond to a variable name defined in the file/object. Sets also colorbar-title for non-`'.gz'`-files if `cb.xlab` is missing. - `cb.title`: character string indicating the title of the colorbar (default is set to date information/empty string if date information is missing.) - `cb.xlab`: character string indicating the x-axis label of the colorbar and `cb.xlab.line` its placement line (default is 0). If not defined, it will be set to `varname` for raster , `ncdf4`-objects and `'.nc'`-files or for `'.gz'`-files to a predefined title in the parameter_definitions -dataset according to the `param`-value. - `lon`: Vector returning longitude coordinates of the area to be plotted, only valable for `obj == 'bathy'`. - `lat`: Vector returning latitude coordinates of the area to be plotted, only valable for `obj == 'bathy'`. - `resolution`: resolution of the bathymetric grid, in minutes (default is 4), only valable for `obj == 'bathy'`. - `keep`: whether to write the data downloaded from NOAA into a file (default is FALSE), only valable for `obj == 'bathy'`. - `savename.bathy`: savename for the bathymetric data file, if not specified set to type 'bathy_lon-lat_res.resolution.dat' or 'bathy_v_area_res.resolution.dat', only valable for `obj == 'bathy'`. - `folder.bathy`: directory where bathymetric data should be saved (default is current working directory), only valable for `obj == 'bathy'`. - `show.colorbar`: weather a colorbar should be plotted for image plots(default is `T`). - ``...``: additional arguments to be passed: - **`region`**: see `v_area`. - **`minv, maxv`**: minimum and maximum z-value to be plotted. If not set, default value from the parameter_definitions -dataset will be applied. Argument is overwritten by `adaptive.vals` and `zlim`. - **`replace.na`**: whether missing values should be replaced by minimum values (default is `FALSE`.) - **`param`**: character string indicating the parameter name for the dataset treatment. See `parameter_definitions` for available parameters. For `'.gz'`-files, `param` is derived from the filename. For non-`'.gz'`-files this value is non-obligatory, but can replace the `varname`-argument and vise versa. See examples. - **`main`**: an overall title for the plot: see title . - **`cbpos`**: letter ("b", "l", "t", "r") indicating the position of the colorbar (bottom, left, top, right). Overwrites `cbx` and `cby` values. - **`cbx`**: the horizontal limits (x1, x2) of the colorbar. If missing and the value can not be reconstructed by the region information (e.g. `v_area`, `'.gz'`-file), the user will be asked for manual colorbar placement. - **`cby`**: the vertical limits (y1, y2) of the colorbar. If missing and the value can not be reconstructed by the region information (e.g. `v_area`, `'.gz'`-file), the user will be asked for manual colorbar placement. - **`nticks`**: number of tick marks for the colorbar (default is 5). - **`pal`**: color map to be plotted (default is the 'jet'-colormap, or in case of `'.gz'`-files derived from the parameter_definitions -dataset. See cmap for available color maps and parameter_definitions for predefined colormaps for different parameters.) - **`sidelabels`**: whether an additional y-axis label and title should be added to the plot device (default is `FALSE`). If `TRUE`, y-axis label is defined by `Ylab`, the additional title is derived from the `date`-information and gives the month information. - **`Ylab`**: an additional title for the y axis (default is date information), only used when `sidelabels` is set `TRUE`. Default value is year-information. - **`axeslabels`**: whether axeslabels should be shown (default is `TRUE`, set as 'longitude' and 'latitude') - **`subplot`**: whether `'.gz'`-file will be plotted as a sub plot to an existing plot device (default is `FALSE`; see: par ) - **`width, height`**: the width and height of the plotting window, in inches. For `'.gz'`-files, default values are derived from the `region`-name as indicated by the filename. See region_definitions for predescribed definitions and use add.region to add new region definitions. - **`figdim`**: numeric vector indicating the `width` and `height` of the plot device in inches. For `'.gz'`-files, default values are derived from the `region`-name as indicated by the filename. Value is overwritten if both, `width` and `height` are provided. See region_definitions for predescribed definitions and use add.region to add new region definitions. - **`xpos`**: integer: initial position of the top left corner of the figure window on the pc-screen, given in pixels. Negative values are from the opposite corner. (default is -1). Disregarded under Mac OS and if `Save` is set `TRUE`. - **`Save`**: whether the a plot device should be saved automatically as an image file of type `fileformat` in a folder specified by `plotfolder` (default is `FALSE`) - **`plotfolder`**: directory where images should be saved (default is current working directory). - **`plotname`**: the name of the output file(s). If not set, value will be derived from the provided file information (For `'.gz'`-files, default `plotname` is equal to the `'.gz'`-filename, replacing the `'.gz'`-fileformat-suffix with the defined image-`fileformat`. - **`fileformat`**: fielformat of image file to be saved (only `png` and `eps` are accepted; default is `png`). - **`suffix`**: suffix to be added to the image filename, before the filetype specification (e.g. '...suffix.png'). - **`v_image`**: whether an image-plot should be plotted (default is `TRUE`) - **`v_contour`**: whether `contour` lines should be plotted (default is `FALSE`). If `levels` are specified, `v_contour` is set `TRUE`. - **`levels`**: numeric vector of levels at which to draw contour lines. - **`contour.labels`**: a vector giving the labels for the contour lines. By default levels are used as labels. - **`v_arrows`**: whether current or wind vectors should be plotted (default is `TRUE`; Argument is disregarded for non-`.gz`-files and omitted if non current or wind data-files are provided) - **`scale_arrow`**: scale factor needed for current and wind vector plots (default is 1; Argument is disregarded for non-`.gz`-files and omitted if no current or wind data-files are provided, indicated by the param-argument (valid `param`-definitions are: 'uz' and 'vz', for current data, 'wu' and 'wz' for wind data)) - **`terrain`**: whether the to keep terrain data (default is `FALSE`). If set `FALSE` and `visualize` is `TRUE`, `grid` command in plotmap is disabled! - **`verbose`**: whether the plot information shall be printed in the R-console (by default `TRUE`) - **`...`**: Additional arguments to be passed to `plotmap` (`bwd`, `fill`, `col`, `border`, `grid`, `grid.res`, `axeslabels`, `ticklabels`, `cex.lab`, `cex.ticks`). ## Details `v` uses the `maps` and `maptools` functions to plot the landmask. See `clim_plot` for aligned plots of satallite-data climatologies. ## See Also `clim_plot, readbin, name_split, regions, plotmap, v` ## Author(s) Robert K. Bauer ## References Bauer, R. K., Stepputtis, D., Grawe, U., Zimmermann, C., and Hammer, C. 2013. Wind-induced variability in coastal larval retention areas: a case study on Western Baltic spring-spawning herring. Fisheries Oceanography, 22: 388-399. ## Examples ```r ################## simple example section: ## Example 1: load & plot a sample Raster-object path <- system.file("test_files", package="oceanmap") load(paste0(path,"/medw4_modis_sst2_4km_1d_20020705_20020705.r2010.0.qual0.Rdata"),verbose=TRUE) dat <- raster::crop(dat,extent(c(0,10,40,44))) ## crop data, xlim/ylim not yet implemented in v() print(dat) v(dat, main="Raster-object", cbpos='r') ## Example 2: load & plot sample netcdf-file ('.nc'-file) nfiles <- Sys.glob(paste0(path,'/*.nc')) # load list of sample-'.nc'-files head(nfiles) ### option a) load netcdf-file with ncdf4-package and plot it library('ncdf4') ncdf <- nc_open(nfiles[1]) # print(ncdf) # v(obj = ncdf, cbpos="r") ### option b) load and plot netcdf-file as RasterStack object # nc <- nc2raster(nfiles[1]) # v(nc,cbpos="r") # plot RasterStack object ### option c) plot netcdf-file directly # v(nfiles[1], cbpos="r") # v(nfiles[1], cbpos="r", replace.na=TRUE) ###### plot multiple layers: # par(mfrow=c(2,2)) # v(nfiles[1], t=1:4, cbpos="r", replace.na=TRUE, subplot = TRUE) # ## Example 2: load & plot bathymetry data from the NOAA-ETOPO1 database # par(mfrow=c(2,1)) # bathy <- get.bathy("medw4", terrain=T, res=3, keep=T, visualize=T, subplot = TRUE, grid=F) # # load('bathy_medw4_res.3.dat',verbose = T); bathy <- h # v(bathy, param="bathy", subplot = TRUE, terrain=F, levels=c(200,2000)) # show contours # # ## b) only contour lines: # par(mfrow=c(1,2)) # h <- get.bathy("lion",terrain=F,res=3, visualize=T, # v_image = FALSE, levels=c(200,2000)) # # ## use v-function for same plot but on subregion: # v(h,v_area = "survey", param="bathy", # v_image = FALSE, levels=c(200,2000)) ## Example 3: plot sample-'.gz'-file gz.files <- Sys.glob(paste0(path,'/*.gz')) # v(gz.files[2]) ## plot content of gz-file ## Example 4: load sample-'.gz'-file manually as Raster-object and plot it obj <- readbin(gz.files[2],area='lion') # par(mfrow=c(1,2)) # v(obj,param="sst",subplot = TRUE) # v(obj,param="Temp",subplot = TRUE) ## note unset "pal" (colormap) for unkown "param"-values! ## Example 5: available color maps data('cmap') # load color maps data names(cmap) # list available color maps gz.files <- Sys.glob(paste0(path,'/*.gz')) # figure(width=15,height=15) # par(mfrow=c(4,5)) # for(n in names(cmap)) v(gz.files[2], v_area='lion', subplot=TRUE, # pal=n, adaptive.vals=TRUE, main=n) ## define new color maps from blue to red to white: n <- colorRampPalette(c('blue','red','white'))(100) # v(gz.files[2], v_area='lion', subplot=TRUE, # pal=n, adaptive.vals=TRUE, main="own colormap") ## Example 6: available parameters data(parameter_definitions) names(parameter_definitions) # ?parameter_definitions # figure(width=12, height=6.2) # par(mfrow=c(2,3)) # v('*sst2*707*',v_area="medw4",main="sst", folder=path, subplot=TRUE) # v('*chla*531*',v_area="medw4",main="chla", folder=path, subplot=TRUE) # v('*chlagrad*',v_area="medw4",main="chlagrad",folder=path, subplot=TRUE) # v('*p100*',v_area="medw4",main="p100 (oceanic fronts)",folder=path, subplot=TRUE) # v('*sla*',v_area="medw4",main="sla",folder=path, subplot=TRUE) # h <- get.bathy("medw4",visualize=TRUE,terrain=F,res=4, subplot=TRUE,main="bathy") ################## advanced example section: ## Example I: plot bathymetry using a v_area-keyword ## requires server connection! # par(mfrow=c(2,1)) # v("bathy","lion",res=4, keep=TRUE,border='grey', # main='Gulf of Lions bathymetry',cb.title="resolution 4 min") # v("bathy","lion",res=1, keep=TRUE,border='grey', # cb.title="resolution 1 min") # can take some time depending on server connection! ## Example II: plot bathymetry of the Baltic Sea defined by longitude and latidtue coordinates ## requires server connection! lon <- c(9, 31) lat <- c(53.5, 66) #v("bathy",lon=lon,lat=lat,main="Baltic Sea") ## Example III: plot landmask of the Baltic Sea defined by an extent- or raster-object ## requires server connection! library('raster') ext <- extent(lon,lat) # v("bathy",ext,main="Baltic Sea",res=4,levels=200) # extent-object ## Example IV: plot '.gz'-files, following default plot-procedure check_gzfiles(folder=path) # return file summary-table gz.files <- Sys.glob(paste0(path,'/*.gz')) # load sample-'.gz'-files # v(gz.files[1:4]) # v(gz.files[4],bwd=2) ## Example V: plot climatologies from '.gz'-files ## (ATTENTION: not working for non-'gz'-files, requiring ImageMagick) # clim_plot('*1s*.gz' ,folder = path,bwd=0.7,adaptive.vals=TRUE,plotname="seasonal_climatology.png") ## Example VI: plot subregion of gz-files as subplots # graphics.off() # par(mfrow=c(2,1)) # v(gz.files[1:2],v_area='lion') # run ?region_definitions to see predefined regions ## Example VII: plot subregion of raster file # all manual: obj <- readbin(gz.files[2],area='lion') dev.new() ticks <- seq(20,30,5) par(mar=c(5,4,5,8)) image(obj,zlim=range(ticks),col=cmap$jet) plotmap('lion',add=TRUE) # add landmask # set.colorbar(ticks=ticks,cb.title='cb.title',cb.xlab='cb.xlab') ## using v, reconstructing region information # obj <- readbin(gz.files[2],area='lion') # v(obj,varname="sst2",cb.title='cb.title',cb.xlab='cb.xlab') # using v for another subregion ncorse <- crop(obj,extent(6,9,40,42)) # v(ncorse,grid.res=1) # v(ncorse,zlim=c(20,30),cbx=c(8.3,8.9),cby=c(40.7,40.8)) # skipping colorbar widget ## Example VIII: Add region by supplying raster-object, colorbar positions and running the widget #add.region(ncorse,cbx=c(8.3,8.9),cby=c(40.7,40.8)) ## Example IX: plot netcdf-files ('.nc'-files) nfiles <- Sys.glob(paste0(path,'/*.nc')) # load sample-'.nc'-files head(nfiles) ## plot herring larval dispersal from Bauer et al. (2013) # par(mfrow=c(2,2)) # v(nfiles[1], subplot=TRUE, t=1:4,minv=0, maxv=1000, adaptive.vals=FALSE, replace.na=TRUE) # par(new=TRUE,mfrow=c(1,1)) # empty.plot(main='herring larval dispersal in the Greifswald lagoon, Germany') # mtext('see Bauer et al. (2013) as reference') # plot bathymetric data (obtained from the Leibniz Institute for Baltic Sea Research Warnemuende) # v(nfiles[2],varname='bathymetry') # following default plot-procedure # v(nfiles[2],varname='bathymetry',pal='haxbyrev',Log=TRUE, cb.xlab='depth [log m]',levels=50) ```

v function