spider2norm {GCDkit} | R Documentation |
Plots a double normalized spiderplot. Trace-element data are first normalized by the given standard,
as usual (see spider
). Then the normalized concentrations are multiplied by a factor
needed to adjust the normalized content of the selected element in each analysis to a desired value
(such as unity). The goal is to eliminate effects of fractional crystallization
(Thompson et al. 1983, Pearce et al. 2005, Pearce and Stern 2006).
spider2norm(rock=WR,norm=NULL,norm2=NULL,ymin=0,ymax=0,which=rep(TRUE,nrow(rock)), legend=FALSE,pch=labels$Symbol,col=labels$Colour,plot=TRUE,join=TRUE,shaded.col="gray", density=-1,angle=0,xaxs="r",fill.col=FALSE,field=FALSE,add=FALSE,...)
rock |
a numeric matrix; the whole-rock data from which will be filtered out those to be normalized. |
norm |
a character string specifying the model. |
norm2 |
name of the variable for the second normalization. |
ymin, ymax |
y range of the diagram. |
which |
specification of the samples to be plotted. |
legend |
logical; if TRUE, room for legend is reserved. |
pch |
a vector specifying the plotting symbols. |
col |
a numeric vector; colour of the plotting symbols and connecting lines. |
plot |
logical; if set to FALSE, individual patterns are not plotted. |
join |
logical; if TRUE, the NAs are extrapolated so that the patterns are unbroken. |
shaded.col |
numeric: colour for the cross-hatched fill. |
density |
numeric: density of the fill pattern (fraction of the whole plotting range). |
angle |
numeric: angle of the fill pattern (in degrees). |
xaxs |
style of the xaxis: see ' |
fill.col |
colour for solid fill |
field |
logical; if TRUE, a shaded field denoting the overall data span is plotted |
add |
logical; if TRUE, a new plot is started (otherwise overplot). |
... |
further graphical parameters: see ' |
The parameter 'norm' is an optional search pattern to
query the available normalizing model names. It can contain a
substring or even a regular expression. For choosing the correct
normalization values serves the auxiliary function
selectNorm
.The function fails
if no matches are found or the search is ambiguous.
See selectNorm
for details.
The samples to be plotted can be selected based on combination of three
searching mechanisms (by sample name/label, range or a Boolean condition) - see
selectSamples
for details.
Then the user is prompted whether to use the currently assigned plotting symbols. If desired so, the symbols and colours can be specified in a simple spreadsheet- like interface.
Likewise the scale of the y axis can be specified interactively.
results |
numeric matrix with normalized concentrations |
.
Vojtech Janousek, vojtech.janousek@geology.cz
Pearce J A, Stern R J (2006) Origin of back-arc basin magmas: Trace element and isotope perspectives. Back-Arc Spreading Systems: Geological, Biological, Chemical, and Physical Interactions. Geophysical Monograph Series 166. American Geophysical Union, pp 63-86
Pearce J A, Stern R J, Bloomer S H, Fryer P (2005) Geochemical mapping of the Mariana arc-basin system: implications for the nature and distribution of subduction components. Geochem Geophys Geosyst 6: doi: 10.1029/2004GC000895 doi: 10.1029/2004GC000895
Thompson R N, Morrison M A, Dickin A P, Hendry G L (1983) Continental flood basalts... Arachnids rule OK? In: Hawkesworth C J, Norry M J (eds) Continental Basalts and Mantle Xenoliths. Shiva, Nantwich, pp 158-185
For the syntax of the setup file with normalizing values and adding new
normalization schemes
see selectNorm
; for further variants of spiderplots, see
spider
, spiderByGroupPatterns
and spiderByGroupFields
.
ee<-spider2norm(WR,"Boynton","Yb",0.1,1000,pch="*",col="red",cex=2) # the ee<- construction redirects the textual output ee<-spider2norm(WR,"Boynton","Yb",field=TRUE,density=0.05,angle=60,col="red",0.1,1000) ee<-spider2norm(WR,"Boynton","Yb",field=TRUE,fill.col=TRUE,shaded.col="khaki",0.1,1000) # Shade the background field portraying the overall variation ee<-spider2norm(WR,"Boynton","Lu",0.1,1000,pch=labels$Symbol,col=labels$Colour,cex=labels$Size) ee<-spider2norm(WR,"Boynton","Lu",field=TRUE,density=0.02,angle=45,col="gray",add=TRUE) # Shade the background field portraying the overall variation ee<-spider2norm(WR,"Boynton","Lu",0.1,1000,pch=labels$Symbol,col=labels$Colour,cex=labels$Size) ee<-spider2norm(WR,"Boynton","Lu",field=TRUE,fill.col=TRUE,shaded.col="gray",add=TRUE) # Possible styles for x axis multiplePerPage(8,nrow=2,ncol=4,"Possible x axis styles", dummy=FALSE) ee<-spider2norm(WR, "Boynton","Yb", 0.1, 1000, pch=labels$Symbol, col=labels$Colour, cex=labels$Size, offset=F, xrotate=F, centered=F,new=F) ee<-spider2norm(WR, "Boynton","Yb", 0.1, 1000, pch=labels$Symbol, col=labels$Colour, cex=labels$Size, offset=F, xrotate=T, centered=F,new=F) ee<-spider2norm(WR, "Boynton","Yb", 0.1, 1000, pch=labels$Symbol, col=labels$Colour, cex=labels$Size, offset=F, xrotate=F, centered=T,new=F) ee<-spider2norm(WR, "Boynton","Yb", 0.1, 1000, pch=labels$Symbol, col=labels$Colour, cex=labels$Size, offset=F, xrotate=T, centered=T,new=F) ee<-spider2norm(WR, "Boynton","Yb", 0.1, 1000, pch=labels$Symbol, col=labels$Colour, cex=labels$Size, offset=T, xrotate=F, centered=F,new=F) ee<-spider2norm(WR, "Boynton","Yb", 0.1, 1000, pch=labels$Symbol, col=labels$Colour, cex=labels$Size, offset=T, xrotate=T, centered=F,new=F) ee<-spider2norm(WR, "Boynton","Yb", 0.1, 1000, pch=labels$Symbol, col=labels$Colour, cex=labels$Size, offset=T, xrotate=F, centered=T,new=F) ee<-spider2norm(WR, "Boynton","Yb", 0.1, 1000, pch=labels$Symbol, col=labels$Colour, cex=labels$Size, offset=T, xrotate=T, centered=T,new=F) spider2norm(WR,"Boynton","Yb",plot=FALSE) # Calculation only