1. Create a new text file and name it “Figure 2 dataset.txt”
2. Copy the data below in the text file; save and close
Patient Difficulty Frequency 0 1 85 0 2 10 0 3 5 0 4 0 0 5 0 1 1 45 1 2 30 1 3 15 1 4 5 1 5 0
3. Open RStudio and create a new R script (Ctrl + Shift + N)
4. Copy the syntax below in the R script
5. Insert the right directory of “Ghostscript” into the 7th line (see R Graphs – Preparation) – use “/” instead of “\” to seperate directory levels
6. Insert the right directory of your dataset (see step 1) into the 8th line – use “/” instead of “\” to seperate directory levels
7. Select all (Ctrl + A) and push the “Run” button
8. You should find your high resolution figure in the same directory as your dataset
Now you are ready to play around – use your own dataset or change the syntax and see what happens.
#### This syntax is written by Ronald Bierings - PhD student Ophthalmology UMCG ####
#### Questions and/or remarks are welcome (ronaldbierings@gmail.com) ####
#=======================================================================================================#
#PREPARATION FIGURE 2
Sys.setenv(R_GSCMD="C:/Program Files/gs/gs9.21/bin/gswin64c.exe") #Install Ghostscript and put the right path here (NB: "/" and not"\")
setwd("D:/Desktop") #Sets directory file (NB: "/" and not"\")
data <- read.table("Figure 2 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=cdata, aes(x=Difficulty, y=Frequency, fill=factor(Patient))) + #Points x and y, group
geom_bar(colour="black", width=.8, stat="identity",position="dodge") + #Bars next to eachother
scale_fill_manual(values=c("white", "black"), labels=c("Controls", "Patients")) + #Colors of bars manually set and labeled
#### AXIS ####
scale_y_continuous(limits = c(0, 100), breaks=seq(0,100,10), expand = c(0,0)) + #Axis minimum, maximum, breaks
scale_x_continuous( #Log axis minimum, maximum, breaks
breaks=seq(1,5,1), #Breaks x-axis (5 groups)
labels = c("No \n difficulty \n","A little \n difficulty \n","A lot of \n difficulty \n","Extreme \n difficulty \n", "Stopped \n doing \n")
) +
#### TITLE / UNIT and QUANTITY ####
ggtitle("") + #No title above graph
xlab(expression("Seeing outside on a cloudy day")) + #x-axis label
ylab("Frequency (%)") #y-axis label
#### LAY-OUT ####
fig2 =
p +
annotate("text", x = 0.6, y = 94, label = "Figure 2", size = 8, hjust=0, fontface=2) + #Title within graph (bold)
theme_bw() +
theme(
axis.ticks.x = element_blank(), #No x-axis ticks
axis.ticks.y = element_line(colour="black"), #No y-axis ticks
panel.border = element_rect(colour = "black"), #Black border surrounding graph
panel.grid.major.x = element_blank() , #No vertical gridlines
panel.grid.major.y = element_line(colour = "gray95"), #Major grid lines
panel.grid.minor = element_blank(), #No minor grid lines
axis.line = element_line(colour = "black"), #Lay-out axis lines
axis.title.x=element_text(size=25, colour="black"), #Lay-out x-axis title
axis.title.y=element_text(size=25, colour="black"), #Lay-out y-axis title
axis.text.x=element_text(size=20, colour="black"), #Lay-out x-axis text
axis.text.y=element_text(size=20, colour="black"), #Lay-out y-axis text
legend.text = element_text(size = 20), #Legend size
legend.position = c(0.85,0.907 ), #Legend position (x,y)
panel.background = element_rect (fill = "white"), #Background color
legend.background = element_blank(), #Legend text background color
legend.key=element_blank(), #Legend shapes background color
legend.key.size = unit(2, 'lines'), #Space between legend categories
legend.title = element_blank (), #Legend title
plot.margin = unit(c(0,0.2,0.1,0.1), "in") #Margins
)
fig2 #Show the figure you just created
#########################
#=======================================================================================================#
################################ SYNTAX TO SAVE GRAPH AS HQ TIFF ##################################
bitmap("Figure 2.tiff", width = 7.5, height = 7.5, units = 'in', type="tifflzw", res=600)
grid.arrange(fig2, 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 in the directory of your database and find Figure 2.tiff ####
#=======================================================================================================#
Ronald Bierings 