Make sure you downloaded Figure 1 – Dataset.
Follow the steps below to create Figure 1.
1. Open RStudio
2. Push Ctrl + Shift + N (creates a new R script)
3. Copy the syntax below in the R script
4. Insert the right directory of your dataset into the 8th line
5. Insert the right directory of “Ghostscript” into the 89th line
5. Select all (Ctrl + A) and push the “Run” button
6. You should find the high quality picture on your Desktop
#### This syntax is written by Ronald Bierings - PhD student Ophthalmology UMCG ####
#### Questions and/or remarks are welcome (ronaldbierings@gmail.com) ####
#=======================================================================================================#
#### LOADING AND PREPARATION OF YOUR DATA ####
setwd("H:/desktop") #Sets directory file (NB: "/" and not"\")
data <- read.table("Figure 1 - Dataset.txt",header=T) #Loads dataset
attach(data) #Makes dataset active
names(data) #Shows names of variables
summary(data) #Gives summary of dataset
data #Gives whole dataset
Patients <- factor(Patients) #Categorical variable (standard: quantitative)
library("ggplot2") #Loads package
library("Rmisc") #Loads package
library("plyr") #Loads package
library("scales") #Loads package
library("gridExtra") #Loads package
library("cowplot") #Loads package
#=======================================================================================================#
###################################### SYNTAX TO PLOT GRAPH #######################################
#### POINTS / ERRORBARS / LINES ####
p=ggplot(
data, aes(x=D, y=mean, group=Patients)) + #Points x and y, group
geom_errorbar(aes(ymin=mean-se, ymax=mean+se), width=.2) + #Errorbars
geom_line(linetype = 2, size = 1)+ #Line between points
geom_point(aes(shape=factor(Patients)), size=6,fill="white") + #Groups have different shapes
scale_shape_manual(values=c(16,21), labels=c("Controls", "Patients")) + #Shapes manually set and labeled
#### AXIS ####
scale_y_continuous(limits = c(-0.5, 1.6), breaks=seq(-1,2,0.5)) + #Y-axis, limits, breaks/labels
scale_x_log10( #X-axis (log)
breaks = scales::trans_breaks("log10", function(x) 10^x,n=5), #Breaks x-axis
labels = scales::trans_format("log10", scales::math_format(10^.x)) #Labels x-axis
) +
#### R TITLE / UNIT and QUANTITY ####
ggtitle("") + #No title above graph
xlab(expression("Luminance "(cd/m^2) )) + #x-axis label
ylab("log CS") #y-axis label
#### LAY-OUT ####
fig1=
p +
annotate("text", x = 0.01, y = 1.5, label = "Figure 1", size = 8, hjust=0, fontface=2) + #Title within graph (bold)
annotate("text", x = 0.01, y = 1.5, label = " Psychophysical laws", size = 8, hjust=0) + #Title within graph
theme_bw() +
theme(
panel.border = element_rect(colour = "black", size = 1), #Black border surrounding graph
panel.grid.major = element_line(colour = "gray95", size=1), #Major grid lines
panel.grid.minor = element_blank(), #Minor grid lines
axis.title.x=element_text(size=25, colour="black", vjust=-0.5), #Lay-out x-axis title
axis.title.y=element_text(size=27, colour="black"), #Lay-out y-axis title
axis.text.x=element_text(size=23, colour="black"), #Lay-out x-axis text
axis.text.y=element_text(size=23, colour="black"), #Lay-out y-axis text
axis.ticks.x = element_line(colour="black", size=0.5), #Lay-out x-axis ticks
axis.ticks.y = element_line(colour="black", size=0.5), #Lay-out y-axis ticks
legend.position = c(0.8,0.135 ), #Legend position (x,y)
legend.text = element_text(size = 20), #Legend background
panel.background = element_rect (fill = "white"), #Background color of graph
legend.background = element_blank(), #No background color legend
legend.key=element_blank(), #No background color legend
legend.key.size = unit(2, 'lines'), #Some space between legend keys
legend.title = element_blank (), #No legend title
plot.margin = unit(c(0,0.2,0.1,0.1), "in") #Margins (top, right, bottom, left)
) +
annotation_logticks(sides = "bt", base=10, size =1) #Log ticks on sides
fig1 #show the figure you just created.
#=======================================================================================================#
################################ SYNTAX TO SAVE GRAPH AS HQ TIFF ##################################
Sys.setenv(R_GSCMD="C:/Program Files/gs/gs9.21/bin/gswin32c.exe") #Install Ghostscript and put the right path here
bitmap("Figure 1.tiff", width = 7.5, height = 7.5, units = 'in', type="tifflzw", res=600) #Set width and change height to make graphs squared
grid.arrange(fig1, nrow =1, ncol=1, widths=c(1)) #Creats a grid (more applicable if you want more graphs)
dev.off()
par(mfrow = c(1,1))
####Look on your Desktop and find Figure 1.tiff ####
#=======================================================================================================#
Ronald Bierings 