#Leaves analyses

#https://momx.github.io/Momocs/articles/Momocs_intro.html

#~~~
#1. Generate template for leaves morphometry
#~~~

Plant_ID <- c("GH_1042", "GH_0501", "GH_0294", "", "", "", "", "", "", "")

##Template for leaves morphometry
pdf(paste0("Input_sheets_leaves/Leaves_", Sys.Date(),  "_C.pdf"))
plot(x=0,y=1, xlim = c(0,6), ylim = c(-8,32), type = 'n', frame.plot=F, axes = F, xlab="", ylab="")

#Establish grid
# - 3 columns and 10 rows
nrows <- 10
segments(x0=0, x1=6, y0=seq(0,30,by=3), y1=seq(0,30,by=3))
#Add the last line
segments(x0=0, x1=6, y0=0, y1=0)

ncols <- 3
for(i in 1:ncols){
  segments(x0=i*2, x1=i*2, y0=0, y1=31)
}

#Label columns
text(x=c(1,3,5), y=rep(31,3), c("Plant_ID", "A", "B"), cex=.8)

#Add Plant_IDs
text(x=rep(1, length(Plant_ID)), y=seq(from=1.5, to=30, by=3), Plant_ID, cex=.8)

#Add dots to align petioles
points(x=rep(3.5, nrows), y=seq(from=1.5, to=30, by=3), pch=16, cex=.4)  
points(x=rep(5.5, nrows), y=seq(from=1.5, to=30, by=3), pch=16, cex=.4)  


note <- "NOTE: Glue 2 leaves per ind. in each cell with abaxial surface up and position it horizontally with petiole on dot (stay as straight as possible). 
Scan @600dpi using lab computer and save file as jpg as follows: Leaves_sagebrush_stomata_project_YYYYMMDD.jpg."
text(x=0, y=-3, paste(strwrap(note,width=150), collapse='\n'), cex=.5, adj=0)

#Add date
text(x=6, y=32.5, paste0("Date: ", Sys.Date()), cex=.6, adj=1)

dev.off()

#~~~
#2. Process scanned image of leaves
#~~~


#Load packages

require(magick)
require(sp)
require(image.ContourDetector)
require(imager)
require(Momocs)

library(CropDetectR)
library(imager)
library(ggplot2)
library(dplyr)
library(reshape2)
library(EBImage)
library(stats)

###~~~
#Read masterfile in csv
###~~~
csv <- read.csv("DB_leaves_morpho_GH.csv")

###~~~
#Process images from scans - to BW
###~~~

for(i in 1:nrow(csv)){
  #Load image
  img <- magick::image_read(paste(as.vector(csv$Folder[i]), "/", as.vector(csv$Scan_jpg[i]), sep=''))
  
  #Process A
  plantA <- magick::image_crop(img, as.vector(csv$Coordinates_A[i]))
  plantABW <- plantA %>% 
    magick::image_convert(colorspace = "Gray") %>%
    magick::image_threshold(type = "white", threshold = "56%") %>%
    magick::image_threshold(type = "black", threshold = "56%")
  #Write image
  magick::image_write(plantABW, path = paste0("BW_leaves_individual/GH_", as.vector(csv$Seedling_ID[i]), "_A.jpg"))
  
  plantB <- magick::image_crop(img, as.vector(csv$Coordinates_B[i]))
  plantBBW <- plantB %>% 
    magick::image_convert(colorspace = "Gray") %>%
    magick::image_threshold(type = "white", threshold = "56%") %>%
    magick::image_threshold(type = "black", threshold = "56%")
  #Write image
  magick::image_write(plantBBW, path = paste0("BW_leaves_individual/GH_", as.vector(csv$Seedling_ID[i]), "_B.jpg"))
}

###~~~
#Morphometric analyses on processed images cleaned in Fiji
###~~~
# https://momx.github.io/Momocs/articles/Momocs_intro.html

###
#Load csv with info on leaves
###
csv <- read.csv("DB_leaves_morpho_GH.csv")
#Add a pop col
csv$Pop <- sapply(strsplit(as.vector(csv$Family_ID), "_"), "[[", 1)
#Match images with pop (for plotting info) 
# This vector is used for mapping purposes
facImg <- csv$Pop[match(sapply(strsplit(sapply(strsplit(imgL, split = "GH_"), "[[", 2), "_"), "[[", 1), csv$Seedling_ID)]

###
#Load images in Momocs
###
imgL <- list.files("BW_leaves_individual/", pattern = "_*.jpg", full.names = T)
input <- Momocs::import_jpg(imgL)

datL <- Momocs::Out(x = input, fac = facImg)

###
#Put all images in same system = center
###
datCent <- datL %>%
  coo_center %>% coo_scale %>%
  coo_alignxax() %>% coo_slidedirection("up") 

#Stack all images to observe variation
pdf("Stack_panel_leaves.pdf")
stack(datCent)
panel(datCent, fac=~value, names=NULL)
dev.off()

####
#Fournier analysis of leaf morphologies
###
datCent.f <- efourier(datCent, norm = T)
#Apply model to infer PCA showing how leaf morph cluster
datCent.p <- PCA(datCent.f)
class(datCent.p)        # a PCA object, let's plot it

#Plot PCA by pop: IDT3 and IDT1 express most variability, 
# whereas the other pops are more coherent
#pdf("PCA_fournier_leaves_pop.pdf")
plot_PCA(datCent.p, ~value)
  Momocs::draw_axes(datCent.p)
#dev.off()

  
###
#Leaf areas
###
#Infer shape area (in pixels)
LeafArea <- coo_area(datL)

#Convert to mm2 (= (pixel * 25.4)/dpi=600)
LeafAreammsq <- (LeafArea * 25.4)/600

#Boxplot area by pop
pdf("Figures/Leaf_area_mm_sq_boxplot.pdf")
boxplot(LeafAreammsq ~ facImg, xlab = "Population", ylab = "Leaf area (mm2)")
dev.off()

#GLM
GLMAreaPop <- glm(LeafAreammsq ~ facImg)
#Tukey's test
emmeans::emmeans(GLMAreaPop, specs = pairwise ~ facImg)


#Kmeans analysis
pdf("Figures/Kmeans_5_leaves.pdf")
KMEANS(datCent.p, centers = 5)
dev.off()

#Clustering analysis
#CLUST(datCent.p, ~value)

###~~~
#Code for Scanned_leaves/Leaves_sagebrush_stomata_project_20210608.jpg
###~~~
#Load image
img <- magick::image_read("Scanned_leaves/Leaves_sagebrush_stomata_project_20210610.jpg")

#Plant_ID: 1
plant1A <- magick::image_crop(img, "880x234+2070+3800")
plant1ABW <- plant1A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant1ABW, path = paste0("Momocs/", Plant_ID[1], "_A.jpg"))

plant1B <- magick::image_crop(img, "880x234+3285+3800")
plant1BBW <- plant1B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant1BBW, path = paste0("Momocs/", Plant_ID[1], "_B.jpg"))

#Plant_ID: 2
plant2A <- magick::image_crop(img, "880x234+2070+3557")
plant2ABW <- plant2A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant2ABW, path = paste0("Momocs/", Plant_ID[2], "_A.jpg"))

plant2B <- magick::image_crop(img, "880x234+3265+3557")
plant2BBW <- plant2B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant2BBW, path = paste0("Momocs/", Plant_ID[2], "_B.jpg"))

#Plant_ID: 3
plant3A <- magick::image_crop(img, "880x234+2080+3313")
plant3ABW <- plant3A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant3ABW, path = paste0("Momocs/", Plant_ID[3], "_A.jpg"))

plant3B <- magick::image_crop(img, "880x234+3265+3333")
plant3BBW <- plant3B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant3BBW, path = paste0("Momocs/", Plant_ID[3], "_B.jpg"))

#Plant_ID: 4
plant4A <- magick::image_crop(img, "880x234+2070+3065")
plant4ABW <- plant4A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant4ABW, path = paste0("Momocs/", Plant_ID[4], "_A.jpg"))

plant4B <- magick::image_crop(img, "880x234+3265+3087")
plant4BBW <- plant4B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant4BBW, path = paste0("Momocs/", Plant_ID[4], "_B.jpg"))

#Plant_ID: 5
plant5A <- magick::image_crop(img, "880x234+2070+2822")
plant5ABW <- plant5A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant5ABW, path = paste0("Momocs/", Plant_ID[5], "_A.jpg"))

plant5B <- magick::image_crop(img, "880x234+3265+2822")
plant5BBW <- plant5B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant5BBW, path = paste0("Momocs/", Plant_ID[5], "_B.jpg"))

#Plant_ID: 6
plant6A <- magick::image_crop(img, "880x234+2070+2578")
plant6ABW <- plant6A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant6ABW, path = paste0("Momocs/", Plant_ID[6], "_A.jpg"))

plant6B <- magick::image_crop(img, "880x234+3265+2578")
plant6BBW <- plant6B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant6BBW, path = paste0("Momocs/", Plant_ID[6], "_B.jpg"))

#Plant_ID: 7
plant7A <- magick::image_crop(img, "880x234+2070+2332")
plant7ABW <- plant7A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant7ABW, path = paste0("Momocs/", Plant_ID[7], "_A.jpg"))

plant7B <- magick::image_crop(img, "880x234+3265+2332")
plant7BBW <- plant8B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant7BBW, path = paste0("Momocs/", Plant_ID[7], "_B.jpg"))

#Plant_ID: 8
plant8A <- magick::image_crop(img, "880x234+2070+2142")
plant8ABW <- plant8A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant8ABW, path = paste0("Momocs/", Plant_ID[8], "_A.jpg"))

plant8B <- magick::image_crop(img, "880x234+3265+2087")
plant8BBW <- plant8B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant8BBW, path = paste0("Momocs/", Plant_ID[8], "_B.jpg"))

#Plant_ID: 9
plant9A <- magick::image_crop(img, "880x234+2070+1836")
plant9ABW <- plant9A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant9ABW, path = paste0("Momocs/", Plant_ID[9], "_A.jpg"))

plant9B <- magick::image_crop(img, "880x234+3265+1836")
plant9BBW <- plant9B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant9BBW, path = paste0("Momocs/", Plant_ID[9], "_B.jpg"))

#Plant_ID: 10
plant10A <- magick::image_crop(img, "880x234+2070+1593")
plant10ABW <- plant10A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant10ABW, path = paste0("Momocs/", Plant_ID[10], "_A.jpg"))

plant10B <- magick::image_crop(img, "880x234+3265+1593")
plant10BBW <- plant10B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant10BBW, path = paste0("Momocs/", Plant_ID[10], "_B.jpg"))


###~~~
#Code for Scanned_leaves/Leaves_sagebrush_stomata_project_20210609.jpg
###~~~

Plant_ID <- c("GH_0836", "GH_1191", "GH_0143", "GH_0402", "GH_1117", "GH_0526", "GH_0268", "GH_0114", "GH_0727", "GH_0703")

#Load image
img <- magick::image_read("Scanned_leaves/Leaves_sagebrush_stomata_project_20210609.jpg")

#Plant_ID: 1
plant1A <- magick::image_crop(img, "880x230+2060+3804")
plant1ABW <- plant1A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant1ABW, path = paste0("Momocs/", Plant_ID[1], "_A.jpg"))

plant1B <- magick::image_crop(img, "880x234+3265+3798")
plant1BBW <- plant1B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant1BBW, path = paste0("Momocs/", Plant_ID[1], "_B.jpg"))

#Plant_ID: 2
plant2A <- magick::image_crop(img, "880x234+2060+3618")
plant2ABW <- plant2A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant2ABW, path = paste0("Momocs/", Plant_ID[2], "_A.jpg"))

plant2B <- magick::image_crop(img, "880x234+3265+3618")
plant2BBW <- plant2B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant2BBW, path = paste0("Momocs/", Plant_ID[2], "_B.jpg"))

#Plant_ID: 3
plant3A <- magick::image_crop(img, "880x234+2070+3372")
plant3ABW <- plant3A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant3ABW, path = paste0("Momocs/", Plant_ID[3], "_A.jpg"))

plant3B <- magick::image_crop(img, "880x234+3265+3372")
plant3BBW <- plant3B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant3BBW, path = paste0("Momocs/", Plant_ID[3], "_B.jpg"))

#Plant_ID: 4
plant4A <- magick::image_crop(img, "880x234+2070+3128")
plant4ABW <- plant4A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant4ABW, path = paste0("Momocs/", Plant_ID[4], "_A.jpg"))

plant4B <- magick::image_crop(img, "880x234+3265+3122")
plant4BBW <- plant4B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant4BBW, path = paste0("Momocs/", Plant_ID[4], "_B.jpg"))

#Plant_ID: 5
plant5A <- magick::image_crop(img, "880x234+2070+2880")
plant5ABW <- plant5A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant5ABW, path = paste0("Momocs/", Plant_ID[5], "_A.jpg"))

plant5B <- magick::image_crop(img, "880x234+3265+2880")
plant5BBW <- plant5B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant5BBW, path = paste0("Momocs/", Plant_ID[5], "_B.jpg"))

#Plant_ID: 6
plant6A <- magick::image_crop(img, "880x234+2070+2636")
plant6ABW <- plant6A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant6ABW, path = paste0("Momocs/", Plant_ID[6], "_A.jpg"))

plant6B <- magick::image_crop(img, "880x234+3265+2636")
plant6BBW <- plant6B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant6BBW, path = paste0("Momocs/", Plant_ID[6], "_B.jpg"))

#Plant_ID: 7
plant7A <- magick::image_crop(img, "880x234+2070+2390")
plant7ABW <- plant7A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant7ABW, path = paste0("Momocs/", Plant_ID[7], "_A.jpg"))

plant7B <- magick::image_crop(img, "880x234+3265+2390")
plant7BBW <- plant8B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant7BBW, path = paste0("Momocs/", Plant_ID[7], "_B.jpg"))

#Plant_ID: 8
plant8A <- magick::image_crop(img, "880x234+2070+2142")
plant8ABW <- plant8A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant8ABW, path = paste0("Momocs/", Plant_ID[8], "_A.jpg"))

plant8B <- magick::image_crop(img, "880x234+3265+2142")
plant8BBW <- plant8B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant8BBW, path = paste0("Momocs/", Plant_ID[8], "_B.jpg"))

#Plant_ID: 9
plant9A <- magick::image_crop(img, "880x234+2070+1897")
plant9ABW <- plant9A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant9ABW, path = paste0("Momocs/", Plant_ID[9], "_A.jpg"))

plant9B <- magick::image_crop(img, "880x234+3265+1897")
plant9BBW <- plant9B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant9BBW, path = paste0("Momocs/", Plant_ID[9], "_B.jpg"))

#Plant_ID: 10
plant10A <- magick::image_crop(img, "880x234+2070+1648")
plant10ABW <- plant10A %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant10ABW, path = paste0("Momocs/", Plant_ID[10], "_A.jpg"))

plant10B <- magick::image_crop(img, "880x234+3265+1648")
plant10BBW <- plant10B %>% 
  magick::image_convert(colorspace = "Gray") %>%
  magick::image_threshold(type = "white", threshold = "56%") %>%
  magick::image_threshold(type = "black", threshold = "56%")
#Write image
magick::image_write(plant10BBW, path = paste0("Momocs/", Plant_ID[10], "_B.jpg"))






Moc
plot(imgBIN)



imgBG <- image_fill(imgBW, "yellow", point = "+1+20", fuzz = 20)

imgBW <- image_background(imgBW, color = "yellow")
plot(imgBW)



#Transform into gray scale

mat <- magick::image_data(img, channels = "gray")
mat <- magick::image_data(imgBW, channels = "gray")
mat <- as.integer(mat, transpose = TRUE)
mat <- drop(mat)

#Contourlines

countlines <- image_contour_detector(mat, Q=0)
plot(countlines)


###OLD CODE####
#Add annotation
text(x=0.6, y=8, paste0("Ind. #1: ", Plant_ID[1]), cex=.6, adj=c(1,1))
text(x=0.6, y=7.5, paste0("Ind. #2: ", Plant_ID[2]), cex=.6, adj=c(1,1))
text(x=0.6, y=7, paste0("Ind. #3: ", Plant_ID[3]), cex=.6, adj=c(1,1))


abline(h=4.5, col = "gray")
abline(h=2.5, col = "gray")

text(x=0.1, y=0.8+(5.5-4.5)/2, "Ind. #3", cex=.6, adj=1, srt=45)
text(x=0.1, y=3.3+(5.5-4.5)/2, "Ind. #2", cex=.6, adj=1, srt=45)
text(x=0.1, y=5.8+(5.5-4.5)/2, "Ind. #1", cex=.6, adj=1, srt=45)

note <- "NOTE: Glue 2 leaves per ind. in each cell with abaxial surface up and position it horizontally with the petiole on the left dot and blade on the second dot (try to stay as straight as possible). 
Scan @600dpi using lab PC computer and save file as jpeg as follows: Leaves_sagebrush_stomata_project_MM_DD_YYYY.jpeg."
text(x=0.05, y=0.1, paste(strwrap(note,width=115), collapse='\n'), cex=.6, adj=0)


#Bottom row
rect(xleft = 0.5, xright = 1.5, ybottom = 0.5, ytop = 1.5)
rect(xleft = 3, xright = 4, ybottom = 0.5, ytop = 1.5)

#Middle row
rect(xleft = 0.5, xright = 1.5, ybottom = 3, ytop = 4)
rect(xleft = 3, xright = 4, ybottom = 3, ytop = 4)

#Top row
rect(xleft = 0.5, xright = 1.5, ybottom = 5.5, ytop = 6.5)
rect(xleft = 3, xright = 4, ybottom = 5.5, ytop = 6.5)

#Add points in the middle of cells
points(x=0.5+(1.5-0.5)/2, y=0.5+(5.5-4.5)/2, cex=.2)
points(x=0.5+(1.5-0.5)/2, y=3+(5.5-4.5)/2, cex=.2)
points(x=0.5+(1.5-0.5)/2, y=5.5+(6.5-5.5)/2, cex=.2)

points(x=0.8+(1.5-0.5)/2, y=0.5+(5.5-4.5)/2, cex=.2)
points(x=0.8+(1.5-0.5)/2, y=3+(5.5-4.5)/2, cex=.2)
points(x=0.8+(1.5-0.5)/2, y=5.5+(6.5-5.5)/2, cex=.2)


points(x=3+(1.5-0.5)/2, y=0.5+(5.5-4.5)/2, cex=.2)
points(x=3+(1.5-0.5)/2, y=3+(5.5-4.5)/2, cex=.2)
points(x=3+(1.5-0.5)/2, y=5.5+(6.5-5.5)/2, cex=.2)

points(x=3.3+(1.5-0.5)/2, y=0.5+(5.5-4.5)/2, cex=.2)
points(x=3.3+(1.5-0.5)/2, y=3+(5.5-4.5)/2, cex=.2)
points(x=3.3+(1.5-0.5)/2, y=5.5+(6.5-5.5)/2, cex=.2)


#Leaf label/rep
text(x=0.3, y=0.5+(5.5-4.5)/2, "A")
text(x=0.3, y=3+(5.5-4.5)/2, "A")
text(x=0.3, y=5.5+(6.5-5.5)/2, "A")

text(x=2.8, y=0.5+(5.5-4.5)/2, "B")
text(x=2.8, y=3+(5.5-4.5)/2, "B")
text(x=2.8, y=5.5+(6.5-5.5)/2, "B")