crop.plot2d: A two dimensional plot (xy scatterplot) of linear...

In elizabethastroud/Cropprocessing: Data organisation, classification and visualisation of archaeobotanical data to understand crop processing stage

A two dimensional plot (xy scatterplot) of linear discriminant scores from LDAcrop.pro

Description

This function plots the linear discriminant scores from LDAcrop.pro as a 2D graph.

Usage

crop.plot2D(x,ylims=NULL,xlims=NULL,gcol=NULL, gbg=NULL,gpch=NULL, col ='black', bg="black", pch=15,site="Site", Func1=1, Func2=2, label=NULL, pos=c(0,-0.3), lab.col= "black", lab.cex = 0.8)

Arguments

x	dataframe containing columns with the LD1, LD2 and LD3 scores - this can be the output of LDAcrop.pro, see details for further information
ylims	The limits of the y axis (expressed as c(min, max))
xlims	The limits of the x axis (expressed as c(min, max))
gcol	Symbol colours of the ethnographical crop processing groups written as c("red", "green"...) etc. The default produces a black and white plot
gbg	The colour of the background of the symbols of the ethnographical crop processing groups (expressed c("red", "green"...) etc. The default produces a black and white plot)
gpch	The symbols of the ethnographical crop processing groups (expressed as c(1, 2, 3, 14, 18))
col	Symbol colour for archaeobotanical data
bg	The background(fill) colours for open plot symbols with a pch = 21:25, see points
pch	Symbol of the archaeobotanical data
site	The name the archaeobotanical data will be labelled as in the legend
Func1	The linear discriminant function to be plotted on the x axis- the default is 1
Func2	The linear discriminant function to be plotted on the y axis- the default is 2
label	The name of the sample(s) to be labelled on the graph
pos	The position of the label (format c(x,y))
lab.col	need to fill
lab.cex	need to fill

Details

The data frame entered as argument x can be the output of LDAcrop.pro or from manual normalizing. However the data frame must have column labelled LD1, LD2, LD3 containing the linear discriminant scores for function 1, 2 and 3

Author(s)

Elizabeth Stroud

References

PAPER reference

Examples

##Example dataset

LD1<-runif(40, min= -0, max=3)
LD2<-runif(40, min = -2, 4)
LD3<-runif(40, min = 2, 4)
Study<-sample(1:3, 40, replace=TRUE)
data<-data.frame(Study,LD1, LD2, LD3)

###Use with defaults (will return a black and white graph)

crop.plot2D(data)

###Changing whcih discriminant function is ploted

crop.plot2D(data, Func1=2, Func2=3)

##Use with colour and symbol variables

crop.plot2D(data, xlims = c(-5, 5), ylims =c(-5,5), gcol =c("forestgreen", "blue",
"skyblue", "orange"), gpch=c(6,7,8,9), col = "darkred", pch = 20 , site ="Example")
  

elizabethastroud/Cropprocessing documentation built on Sept. 27, 2024, 3:03 p.m.