[R] Help with PCA data file prep and R code

[Sarah Stinson]

Hello DRUGs,
I'm new to R and would appreciate some expert advice on prepping files for,
and running, PCA...

My data set consists of aquatic invertebrate and zooplankton count data and
physicochemical measurements from an ecotoxicology study. Four chemical
treatments were applied to mesocosm tanks, 4 replicates per treatment (16
tanks total), then data were collected weekly over a 3 month period.

I cleaned the data in excel by removing columns with all zero values, and
all rows with NA values.
All zooplankton values were volume normalized, then log normalized. All
other data was log normalized in excel prior to analysis in R. All vectorss
are numeric. I've attached the .csv file to this email rather that using
dput(dataframe). I hope that's acceptable.

My questions are:

1. Did I do the cleaning step appropriately? I know that there are ways to
run PCA's using data that contain NA values (pcaMethods), but wasn't able
to get the code to work...
(I understand that this isn't strictly an R question, but any help would be
appreciated.)
2. Does my code look correct for the PCA and visualization (see below)?

Thanks in advance,
Sarah

#read data
mesocleaned <- read.csv("MesoCleanedforPCA.9.16.16.csv")

#run PCA
meso.pca <- prcomp(mesocleaned,
                   center = TRUE,
                   scale. = TRUE)

# print method
print(meso.pca)

#compute standard deviation of each principal component
std_dev <- meso.pca$sdev

#compute variance
pr_var <- std_dev^2

#check variance of first 10 components
pr_var[1:10]

#proportion of variance explained
prop_varex <- pr_var/sum(pr_var)
prop_varex[1:20]

#The first principal component explains 12.7% of the variance
#The second explains 8.1%

#visualize
biplot(meso.pca)

#for visualization, make Treatment vector a factor instead of numeric
meso.treatment <- as.factor(mesocleaned[, 3])

#ggbiplot to visualize by Treatment group
#reference: https://www.r-bloggers.com/computing-and-visualizing-pca-in-r/

library(devtools)
install_github("ggbiplot", "vqv")
library(ggbiplot)

print(ggbiplot(meso.pca, obs.scale = 1, var.scale = 1, groups =
meso.treatment, ellipse = TRUE, circle = TRUE))
g <- ggbiplot(meso.pca, obs.scale = 1, var.scale = 1,
              groups = meso.treatment, ellipse = TRUE,
              circle = TRUE)
g <- g + scale_color_brewer(name = deparse(substitute(Treatments)), palette
= 'Dark2') #must change meso.treatment to a factor for this to work
g <- g + theme(legend.direction = 'horizontal',
               legend.position = 'top')
print(g)

#Circle plot
#plot each variables coefficients inside a unit circle to get insight on a
possible interpretation for PCs.
#reference: https://www.r-bloggers.com/computing-and-visualizing-pca-in-r/

theta <- seq(0,2*pi,length.out = 100)
circle <- data.frame(x = cos(theta), y = sin(theta))
p <- ggplot(circle,aes(x,y)) + geom_path()

loadings <- data.frame(meso.pca$rotation,
                       .names = row.names(meso.pca$rotation))
p + geom_text(data=loadings,
              mapping=aes(x = PC1, y = PC2, label = .names, colour =
.names)) +
  coord_fixed(ratio=1) +
  labs(x = "PC1", y = "PC2")