panelcode

###########################################################################
#########This script contains code and examples       #####################
#########for making scientific quality figures.       #####################
###########################################################################


#read in example dataset
setwd('/Users/lmccullo/Google Drive/LM_root_paper')
ak<- read.csv("ViPER_roots_2015_LM.csv")
akk<- read.csv("ViPER_Root_Agg.csv")
t<- read.csv("agg_temp_15cm.csv")
tt<- read.csv("agg_temp_10cm.csv")

#######################################################
######## Make a multipanel figure #####################
#######################################################
#this code makes a multipanel figure in a jpeg
#that will have manuscript quality label sizes.
#it uses the example dataset to generate the figure
#but it can be changed to any type of data.

#1. specify the directory where you will save your plots
plotDir <- '/Users/lmccullo/Google Drive/Alaska2015/Figures'

#2. specify the number of panels you will need in your plot
pN <- 12

#3. specify how many columns of panes you want
pC <- 4

#4. specify width and height of the panels
#these numbers will depend on how big you make your jpeg
#if they are too big of a size for the jpeg, you will get
#a figure region too big
wd <- 100
hd <- 35

#5. Declare the boundries of each plot limits. This way
#you can readily alter the plot limits without having
#to change anything by hand

#I am going to make a panel of relative humidity and 
#temperature across each hourfor each of my sites. 
#Each site has a different time period.
#I will stack the graphs so that each column in the
#panel is a site since it shares the same values on 
#the x axis.
#x axis limits

#axis soil c:n ratio
xl1	<- 0
xh1 <- 50
#x axis soil temperature to 10 cm
xl2 <- -4
xh2 <- 6
#%moss cover
xl3 <- 0
xh3 <- 55
#organic soil moisture
xl4 <- 110
xh4 <- 900
#Live to dead ratio
ylR <- 0
yhR <- 33

#axis label sequences
ysT <- seq(0,33, by=3)
ysR <- seq(0,33, by=3)
xs1 <- seq(0,50,by=5)
xs2 <- seq(-4,6,by=1)
xs3 <-seq(0,55,by=5)
xs4 <-seq(110,900, by = 100)


#character expansions
#cex for plot symbols
cP <- 8
#for y axis
cAy <- 5
#for axis labesl
clabel <- 6
#for x axis
cAx <- 4

#colors for plot symbols
col1 <- "royalblue3"
col2 <- "tomato3"

#line thickness
lw <- 3

#panel letter size and location
#cex for letter label
cl <- 8
#offset from panels
l.offs <- .1
l.offT <- 1
l.offR <-.05


#6. Start generating the plot
#this command will start plotting to file, and anything after it will go to your file.
#It can only be ended with the dev.off() function.
#the plot will be generated into the directory plotDir indicated above
jpeg(paste0(plotDir, "//multipanel1.jpg"), width=100000, height=100000, units="px", quality=100)	
####################################################
############ jpeg            #######################
####################################################
#jpeg(file.name and path, width=width of file, height=height of file,
#     units="px" indicated pixel units, quality=100 (lower numbers will produce lower quality))

# 7. specify the panel layout
#the layout is based on the number of panels declared above  (pn),
#the number of columns specified above (pc), and the width and height
#of each panel (wd, hd respectively) that was specified above
layout(matrix(seq(1,pN), byrow=FALSE, ncol=pC), width=rep(lcm(wd),pN), height=rep(lcm(hd),pN))
####################################################
############ layout          #######################
####################################################
#layout(matrix that is structured to the layout of the panels that contains the plot
#order for each panel, width=widths for each panel, height=heights for each panel)
# 8. start making the plot for panel 1: high density Temp
#8.A. Specify that there should be no margins to the plot
par(mai=c(0,0,0,0))

#8.B. Make an empty plot with the proper limits above
# all points, labels, and axes will be added in seperately.

plot(c(0,1),c(0,1), type="n", xlim=c(xl1,xh1), ylim=c(ylT,yhT), axes=FALSE, xlab=" ",
     ylab=" ", xaxs="i", yaxs="i")

#8. C. add the points that we want to plot
points(tt$soilc.n,tt$fine.dead.live, type="b",
       col=col1,  lwd=lw, cex=cP, pch=19)

#8. D. make axis for y axis	
axis(2, ysT, cex.axis=cAy, las=2, lwd.ticks=3)

#8. E. add a letter to label the panel
text(xl1+l.offs,yhT-l.offT, "A", cex=cl)

#8. F. label the y axis
mtext("Dead:Live biomass", side=2, cex=clabel, line=15)

#8. G. make a box around the plot
box(which="plot")

#8. H. label the site
mtext("Soil C:N", side=1, cex=clabel, line=5)

# 9. start making the plot for panel 2: high density RH
#9.A. Specify that there should be no margins to the plot
par(mai=c(0,0,0,0))	

#9.B. Make an empty plot with the proper limits above
# all points, labels, and axes will be added in seperately.

plot(c(0,1),c(0,1), type="n", xlim=c(xl2,xh2), ylim=c(ylT,yhT), axes=FALSE, xlab=" ",
     ylab=" ", xaxs="i", yaxs="i")

#9. C. add the points that we want to plot
points(tt$temp,tt$fine.dead.live, type="b",
       col=col1,  lwd=lw, cex=cP, pch=19)

#9. D. make axis for y axis	
axis(2, ysR, cex.axis=cAy, las=2, lwd.ticks=3)	


#9. E. add a letter to label the panel
text(xl1+l.offs,yhR-l.offR, "B", cex=cl)

#9. F. label the y axis
mtext("Soil Temperature to 10 cm (C)", side=2, cex=clabel, line=15)

#9. G. make a box around the plot
box(which="plot")

#9. H. make labels for the xaxis
#x axis labels don't get offset from the axis as well in jpeg file set up.
#they will be set up a little differently
#first add axis ticks
axis(1, xs1, rep(" ", length(xs1)),  lwd.ticks=3)
mtext(xs1, at=xs1, side=1, line=4, cex=cAx)

#9. I. add an outer label for both bottom panels since they have the same measure
mtext("Ratio of Fine Dead to Live biomass", side=1, outer=TRUE, line=-7, cex=clabel)

# 10. start making the plot for panel 3: low density Temp
#10.A. Specify that there should be no margins to the plot
par(mai=c(0,0,0,0))

#10.B. Make an empty plot with the proper limits above
# all points, labels, and axes will be added in seperately.

plot(c(0,1),c(0,1), type="n", xlim=c(xl2,xh2), ylim=c(ylT,yhT), axes=FALSE, xlab=" ",
     ylab=" ", xaxs="i", yaxs="i")

#10. C. add the points that we want to plot
points(tt$m.cov, tt$fine.dead.live, type="b",
       col=col2,  lwd=lw, cex=cP, pch=19)


#10. D. add a letter to label the panel
text(xl2+l.offs,yhT-l.offT, "C", cex=cl)	

#10. E. make a box around the plot
box(which="plot")

#10. F. label the site
mtext("%Moss Cover", side=3, cex=clabel, line=5)

# 11. start making the plot for panel 2: high density RH
#11.A. Specify that there should be no margins to the plot
par(mai=c(0,0,0,0))	

#11.B. Make an empty plot with the proper limits above
# all points, labels, and axes will be added in seperately.

plot(c(0,1),c(0,1), type="n", xlim=c(xl2,xh2), ylim=c(ylR,yhR), axes=FALSE, xlab=" ",
     ylab=" ", xaxs="i", yaxs="i")

#11. C. add the points that we want to plot
points(tt$org.moisture, tt$fine.dead.live, type="b",
       col=col2, lwd=lw, cex=cP, pch=19)


#11. D. add a letter to label the panel
text(xl2+l.offs,yhR-l.offR, "D", cex=cl)

#11. E. make a box around the plot
box(which="plot")

#11. F. make labels for the xaxis
#x axis labels don't get offset from the axis as well in jpeg file set up.
#they will be set up a little differently
#first add axis ticks
axis(1, xs2, rep(" ", length(xs2)),  lwd.ticks=3)
mtext(xs2, at=xs2, side=1, line=4, cex=cAx)

plot
#12. turn off plot
dev.off()