multifluo (version 1.1)

plotpca: Plotting a Principal Component Analysis

Description

Plots the Principal Component Analysis from the pca function, and custumizes the output with

Usage

plotpca(x,map="b",n="a",l=0.05,col=NULL,calc="Chi",epd=NULL,et="bar",dif="n",dax="all")

Arguments

x

results of pca

map

if "bil", biplot is plotted with supplementary individuals projected, and labels of supplementary individuals are written if "bip", biplot is plotted with supplementary individuals projected, and points of supplementary individuals are plotted if "b", biplot is plotted if "til", two-way pca is plotted with supplementary individuals projected, and labels of supplementary individuals are written if "tip", two-way pca is plotted with supplementary individuals projected, and la points of supplementary individuals are plotted if "t", two-way pca is plotted

n

number of axes to plot. By default, "a", which calculates an automatic theoretical number of dimensions (when the contribution of loadings is higher than 1)

l

by default 0.05. Risk to be taken in the agreement ellipses

et

"bar" for the confidence ellipses around the product means "ind" for the representation of a proportion of 1-alpha of the panelist scores

col

select the colors of the different individuals

calc

"Chi", "F" or "Sas". Indicates the type of ellipse to be calculated.

epd

when a biplot is chosen, the arrows can be oversized.

dif

if "n", no tests are run if "h", hotelling test is run to detect differences between zones. if "hc", the p-value is corrected with the bonferroni Correction (l is divided by k(k+1)/ where k is the number of zones) if "s", srivastava test is run to detect differences between zones. if "sc", the p-value is corrected with the bonferroni Correction (l is divided by k(k+1)/ where k is the number of zones)

When a test is run, zones not significantly difference are related by a segment

dax

if "all", the test is run on all the Principal Components. If "sig", it is done only on the significant Principal Components. dax can also be a vector determining the index of Principal Component to be chosen for the test (ex dax=c(1,2)).

Examples

# NOT RUN {
data(df.scaled)
resPCA=pca(data=df.scaled[,-1], zone="zone",pixel="pixel")
couleurs=find.colors(rownames(resPCA$IndivCoord)) 
# }
# NOT RUN {
plotpca(x=resPCA)
# }
# NOT RUN {
# }