spider {GCDkit}R Documentation

Spider plot(s): Selected samples

Description

Normalization of trace-element data by the given standard and spiderplot plotting.

Usage

spider.individual(new=TRUE)

spider.contour(chondrit = selectNorm(),what=NULL,
colour.palette = "heat.colors", ymin = 0, ymax = 0,
cex = 1,join = TRUE,pch = 15,
main = "",sub = "",offset = TRUE,centered = FALSE,
xrotate = FALSE, xaxs = "r", new = TRUE, legend = TRUE)

spider(rock=WR, chondrit = selectNorm(), ymin = 0, 
ymax = 0, cex = NULL, plot = TRUE, join = TRUE, 
field = FALSE, legend = FALSE, add = FALSE, 
pch = NULL, col = NULL, shaded.col = "gray", 
density = 0.02, angle = 0, main = "", sub = "", 
offset = FALSE, centered = FALSE, xrotate = FALSE,
xaxs = "r", fill.col = TRUE, log = "y", new = TRUE, ...)

Arguments

new

logical; if true, new plotting window is opened.

chondrit

a numeric matrix with one row; the normalizing values.

what

variable name or formula.

colour.palette

variable name or formula.

rock

a numeric matrix; the whole-rock data from which will be filtered out those to be normalized.

ymin, ymax

y range of the diagram.

cex

magnification of the plotting symbols.

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.

field

logical; if TRUE, a shaded field denoting the overall data span is plotted

legend

logical; if TRUE, room for legend is reserved.

add

logical; if FALSE, a new plot is started (otherwise overplot).

pch

a vector specifying the plotting symbols.

col

a numeric vector; colour of the plotting symbols and connecting lines.

fill.col

logical; should be the field of overall variability filled by solid colour?

shaded.col

numeric: colour for the cross-hatched or solid fill.

density

numeric: density of the fill pattern (fraction of the whole plotting range).

angle

numeric: angle of the fill pattern (in degrees).

main

character: the main title for the plot.

sub

character: the subtitle for the plot.

xrotate

logical; shall be the element names on x axis rotated?

offset

logical; shall be the names for odd and even elements shifted relative to each other?

centered

logical; shall be the element names on x axis plotted in between tick marks?

xaxs

style of the xaxis: see 'help(par) for details.

log

which of the axes should be logarithmic?

...

further graphical parameters: see 'help(par) for details.

Details

This is a quite flexible function, a true Mother of All Spiderplots, that can be used in a number of ways. It is employed by functions of the GCDkit system for normalization and plotting individual patterns for selected samples ('spiderplot.r') or each of the groups
('spider by group individual.r'). In 'spiderplot.r' is stored a user interface to 'spider' for plotting individual patterns. spider3.png

Function 'spider' can also serve for plotting the overall compositional ranges (shown as cross-hatched fields or, optionally, semitransparent filled polygons) in a manner similar to function 'spider by group.r'. spider4.png

In 'spiderplot_contour.r' is stored a user interface to 'spider' for plotting individual patterns, in which the plotting symbols is uniform and colour reflects distribution of an independent variable, such as silica contents. The variable (or formula) can be specified using the parameter 'what', the colour scheme by 'colour.palette'. The legal colour schemes are: '"grays","reds","blues",
"greens","cyans","violets","yellows","cm.colors","heat.colors","terrain.colors",
"topo.colors","rainbow", "jet.colors"'. spider1.png

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. For choosing the correct normalization values serves the auxiliary function selectNorm. 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. The exact appearance of the labels to the x axis can be fine tuned by the arguments 'rotate.xlab', 'offset' and 'centered'. See examples. spider9.png

If 'plot=FALSE', not plotting is done, and only the normalized values are returned.

Value

results

numeric matrix with normalized concentrations.

Note

If not specified, the parameters pch, col and cex are set up by default to 0 (circle), black and 1 numeric matrix, respectively. The only exception occurs when the plotting object is WR, when the missing plotting parameters are sought in the dataframe labels, i.e. among the standard plotting properties.

Author(s)

Vojtěch Janoušek, vojtech.janousek@geology.cz;

Vojtěch Erban, erban@sopky.cz, contributed the algorithm hatching closed polygons

See Also

For the syntax of the setup file with normalizing values and adding new normalization schemes
see selectNorm; for further applications of 'spider' see spider2norm, spiderByGroupPatterns and spiderByGroupFields.

Examples

    data(blatna)
    accessVar("blatna")
    
    ee<-spider.contour("Boynton","SiO2","reds",pch="*",cex=1.5,ymin=0.01,ymax=1000)
    # ee<- redirects the output 
    
    spider(WR,"Boynton",0.1,1000,pch="*",col="red",cex=2,join=FALSE) 

    spider(WR[1:11,],"Boynton",1,500,pch=1:11,col=1:11,legend=TRUE)

    spider(WR,"Boynton",field=TRUE,density=0.02,angle=60,col="darkred",fill.col=FALSE,0.1,1000)

    spider(WR,"Boynton",field=TRUE,fill.col=TRUE,shaded.col="khaki",0.1,1000)
        
    # Shade the background field portraying the overall variation 
    spider(WR,"Boynton",0.1,1000)
    spider(WR,"Boynton",field=TRUE,fill.col=TRUE,shaded.col="gray",add=TRUE)

    spider(WR,"Boynton",0.1,1000)
    spider(WR,"Boynton",field=TRUE,density=0.02,angle=45,col="gray",fill.col=FALSE,add=TRUE)

    # Custom normalization scheme
    chon<-c(0.4,4,50,0.8,0.7,10,35,9,340,9,70,8.0)
    chon<-matrix(chon,nrow=1)
    colnames(chon)<-c("K2O","Rb","Ba","Th","Ta","Nb","Ce","Hf","Zr","Sm","Y","Yb")
    rownames(chon)<-"ORG (Pearce et al. 1984)"
    spider(WR,chon,ymin=0.01,col="navy",ymax=1000)

    # Possible styles for x axis
    multiplePerPage(8,nrow=2,ncol=4,"Possible x axis styles", dummy=FALSE)
    spider(WR, "Boynton", 0.1, 1000, 
        offset=FALSE, xrotate=FALSE, centered=FALSE, 
        main="offset=FALSE, xrotate=FALSE, centered=FALSE",new=FALSE)
    spider(WR, "Boynton", 0.1, 1000, 
        offset=FALSE, xrotate=TRUE, centered=FALSE, 
        main="offset=FALSE, xrotate=TRUE, centered=FALSE",new=FALSE)
    spider(WR, "Boynton", 0.1, 1000, 
        offset=FALSE, xrotate=FALSE, centered=TRUE, 
        main="offset=FALSE, xrotate=FALSE, centered=TRUE",new=FALSE)
    spider(WR, "Boynton", 0.1, 1000, 
        offset=FALSE, xrotate=TRUE, centered=TRUE, 
        main="offset=FALSE, xrotate=TRUE, centered=TRUE",new=FALSE)
    spider(WR, "Boynton", 0.1, 1000, 
        offset=TRUE, xrotate=FALSE, centered=FALSE, 
        main="offset=TRUE, xrotate=FALSE, centered=FALSE",new=FALSE)
    spider(WR, "Boynton", 0.1, 1000, 
        offset=TRUE, xrotate=TRUE, centered=FALSE, 
        main="offset=TRUE, xrotate=TRUE, centered=FALSE",new=FALSE)
    spider(WR, "Boynton", 0.1, 1000, 
        offset=TRUE, xrotate=FALSE, centered=TRUE, 
        main="offset=TRUE, xrotate=FALSE, centered=TRUE",new=FALSE)
    spider(WR, "Boynton", 0.1, 1000, 
        offset=TRUE, xrotate=TRUE, centered=TRUE, 
        main="offset=TRUE, xrotate=TRUE, centered=TRUE",new=FALSE)
    plateCexLab(1.5)
    plateRedraw()
    
    spider(WR,"Boynton",plot=FALSE) # Calculation only
    print(results)

[Package GCDkit version 6.1 Index]