# Load the csv file with the information for the plot. 
my_plot <- read_csv("file_for_plot.csv")

coeff <- 100

# Determine the order that the clusters/genera are going to be in the x axis of the plot. 
my_plot$cluster <- factor(my_plot$cluster, levels = c(#LEVELS#)) 

# Initialize a ggplot object. Declare the input data as the loaded csv file. Determine the plot aesthetics. 
ggplot(data=my_plot, mapping=aes(x=cluster)) + 
    	
    	# Determines the type of plot with geom_jitter, with the desired aesthetics and characteristics. This is done for both y axes. 
	geom_jitter(aes(y=CAI, shape=organism, color=group), width=0.3, height=0.05, size=0.8, alpha=0.4) + 
	geom_jitter(aes(y=GC / coeff, shape=organism, color=group), width=0.3, height=0.05, size=0.8, alpha=0.4) +
	
	# Determines the limits of the y axes. 
	coord_cartesian(ylim=c(0, 0.8)) + 
	
	# Determines y axes as continous, specify the axes titles and breaks. 
	scale_y_continuous(
		name="CAI",
		sec.axis = sec_axis(~.*coeff, name="%GC"),
		breaks=seq(0, 0.8, 0.1)
	) + 
	
	# Specifies the shapes of the dots in the plot according to a variable included in the input file.
	scale_shape_manual(values=c("V"=16, "B"=17)) +
	
	# Specifies the colors according to a variable included in the input file.
	scale_color_manual(values=c(#COLORS#)) +
	
	# Determines the theme of the plot. Legend is excluded, as well as the title of the x axis. Y axes titles, axes labels, plot background, plot grid and axes lines are modified to preference. 
	theme(
		legend.position="none",
		axis.title.x=element_blank(),
		axis.title.y=element_text(size=10),
		axis.title.y.right=element_text(size=10),
		axis.text.x=element_text(size=7, angle=90),
		axis.text.y=element_text(size=7),
		axis.text.y.right=element_text(size=7),
		panel.background=element_rect(fill="white"),
		panel.grid.major.x=element_line(color="lightgray", size=0.5),
		panel.grid.major.y=element_line(color="lightgray", size=0.5),
		axis.line=element_line(size=1, color="dimgray")	
	)
	
# Save the plot. Determine the filename and the characteristics the plot has to be saved in. 
ggsave(filename = "plot.png", width = 16, height = 10, dpi = 500, units = "cm")



#LEVELS#

"Arthrobacter","AK","AL","AM*","AN","AO","AP","AQ","AR","AS","AT","AU*","AV","AW*","AX","AY","AZ","FA","FB","FC","FD","FE","FF","FG"
"Streptomyces","BA","BB","BC","BD","BE","BF","BG","BH","BI*","BJ","BK","BL","BM","BN","BO"
"Rhodococcus","CA","CB","CC*"
"Microbacterium","EA","EB","EC","ED","EE","EF","EG","EH","EI","EJ","EK","EL*","EM","GA","GB"
"Faecalibacterium","Faec*","Faec"
"Lactococcus","Lacto*","Lacto"
"Gordonia","A","CD","CQ","CR","CS","CT","CU","CV","CW","CX","CY","CZ","DB","DC","DE","DF","DG","DH","DI","DJ*","DK","DL",
"DM","DN","DO","DP","DQ","DR","DS","DT","DU","DV"

#COLORS#

"R1"="darkorchid4","R2"="orchid3","M1"="blue4","M2"="skyblue3","F1"="chocolate4","F2"="chocolate","L1"="black","L2"="gray62"
"G1"="darkgreen","G2"="green1"
"A1"="deeppink4","A2"="deeppink","S1"="firebrick4","S2"="firebrick1"

Arthrobacter:
- nRCA/CAI:deeppink4
- GC:deeppink

Streptomyces:
- nRCA/CAI:firebrick4
- GC:firebrick1

Gordonia:
- nRCA/CAI:darkgreen
- GC:green1

Faecalibacterium:
- nRCA/CAI:chocolate4
- GC:chocolate

Lactococcus:
- nRCA/CAI:black
- GC:gray62

Microbacterium
- nRCA/CAI:blue4
- GC:skyblue3

Rhodococcus:
- nRCA/CAI:darkorchid4
- GC:orchid3