Data Management

data$"Phytoplankton(cells/uL)" <- data$"Phytoplankton(cells/L)"/1000000
data$"Chlorophyll-a(ug/L)" <- data$"Chlorophyll-a (mg/L)"/1000

library(ggplot2)
WQ <- data[,names(data) %in% c("Tank","pH","Salinity(ppt)","DO(mg/L)", "Temperature(戼㸰C)","TAN(mg/L)","Nitrite(NO2)mg/L")]
WQ2 <- melt(WQ, id="Tank")
WQ2$WQ = WQ2$variable 

Algae <- data[,names(data) %in% c("Tank","Phytoplankton(cells/uL)","Chlorophyll-a(ug/L)")]
Algae2 <- melt(Algae, id="Tank")
Algae2$Algae_Others = Algae2$variable

data$'Time interval'  = data$'Time interval'/10
Time <- data[,names(data) %in% c("Tank","Time interval","Water Exchange(%)")]
Time2 <- melt(Time, id="Tank")

data$"Time interval" <- data$"Time interval"*-1
data$"Tenure2" <- data$"Tenure"/4
data$"Average weight2" <- data$"Average weight"/2
Third <- data[,names(data) %in% c("Tank","Feed rate","necrosis" ,"Gut" ,"Water Exchange(%)", "Time interval","Average weight2","Tenure2")]
Third2 <- melt(Third, id="Tank")

Algae22 <- melt(Algae, id="Tank")
Algae22$Algae = Algae22$variable

Including Plots

a <- ggplot() +
  geom_bar(data=Algae2, aes(x=Tank, y=value, fill=Algae_Others),stat="identity", position=position_dodge(),alpha = 0.5) + 
  geom_point(data=WQ2, aes(x=Tank, y=value,shape=WQ),size=3,color='#999999')+ scale_shape_manual(values=c(15,3,8,1,16,17))+
  geom_line(data=WQ2,aes(x=Tank, y=value,group = variable),color="grey") +
  geom_bar(data=Time2, aes(x=Tank, y=value,fill=variable),stat="identity", position=position_dodge(),alpha = 0.5)+
  ggtitle("WQ + Algae + Water Exchange + Interval")+
  theme(plot.title = element_text(size=14, family = "Times",face="bold"),
        panel.background=element_rect(fill = "snow2"),
        axis.title=element_blank(),
        axis.line = element_line(color="grey84", size = 0.5),
        plot.background = element_rect(fill = "snow1"),
        panel.grid.major = element_blank())
b <- ggplot() +
  geom_point(data=data, aes(x=Tank, y=data$"Phytoplankton(cells/uL)"),size=3) + 
  geom_line(data=data, aes(x=Tank, y=data$"Phytoplankton(cells/uL)",group=1))+
  geom_point(data=Third2, aes(x=Tank, y=value,color=variable),size=2)+
  geom_point(data=Third2, aes(x=Tank, y=value,color=variable),size=6,alpha = 0.3,color="grey")+
  geom_line(data=Third2, aes(x=Tank, y=value,group=variable,color=variable),size=0.7) +
  ggtitle("Phytoplankton(cells/uL)")+
  theme(plot.title = element_text(size=14, family = "Times",face="bold"),
        panel.background=element_rect(fill = "snow2"),
        axis.title=element_blank(),
        axis.line = element_line(color="grey84", size = 0.5),
        plot.background = element_rect(fill = "snow1"),
        panel.grid.major = element_blank(),
        legend.position="bottom") 
c <- ggplot() +
  geom_bar(data=Algae22, aes(x=Tank, y=value, fill=Algae),stat="identity", position=position_dodge(),alpha = 0.5) + 
  geom_point(data=data, aes(x=data$Tank, y=data$"Maturity Index"),size=3,color='#999999')+
  geom_line(data=data, aes(x=data$Tank, y=data$"Maturity Index",group=1),size=0.7) +
  ggtitle("Algae")+
  theme(plot.title = element_text(size=14, family = "Times",face="bold"),
        panel.background=element_rect(fill = "snow2"),
        axis.title=element_blank(),
        axis.line = element_line(color="grey84", size = 0.5),
        plot.background = element_rect(fill = "snow1"),
        panel.grid.major = element_blank())

Package grid

library(grid)
grid.newpage()
# Create layout : nrow = 3, ncol = 2
pushViewport(viewport(layout = grid.layout(nrow = 2, ncol = 1)))
# A helper function to define a region on the layout
define_region <- function(row, col){
  viewport(layout.pos.row = row, layout.pos.col = col)
} 
# Arrange the plots
print(a, vp = define_region(row = 1, col = 1))   # Span over two columns
print(c, vp = define_region(row = 2, col = 1))

Package ggpubr

ggarrange

library(ggpubr)
figure <- ggarrange(b,c,ncol = 1, nrow = 2,labels = c("B", "C"),heights = c(1.2,1))
annotate_figure(figure,
                top = text_grob("Visualizing", color = "red", face = "bold", size = 14),
                bottom = text_grob("Data source: \n xx data set", color = "blue", hjust = 1, x = 1, face = "italic", size = 10),
                left = text_grob("Figure arranged using ggpubr", color = "green", rot = 90),
                right = "Right Comment", fig.lab = "Figure 1", fig.lab.face = "bold")

ggtext

library(ggpubr)
data("mtcars")
df <- mtcars
df$cyl <- as.factor(df$cyl)
df$name <- rownames(df)
# Textual annotation
# Add rectangle around label
ggtext(df, x = "wt", y = "mpg",
color = "cyl", palette = c("#00AFBB", "#E7B800", "#FC4E07"),
label = "name", repel = TRUE, label.rectangle = TRUE)

ggtexttable

Plot with multiple datasets; dual axis

###Method 1
ggplot()+
  geom_bar(data=data2m, aes(x=Tank-0.24, y=value*900/13880000, group=variable, fill=variable),stat="identity",width=0.45)+
  geom_bar(data=data, aes(x=Tank+0.24,y=data$"Phytoplankton(cells/L)"*900/13880000,group=1),stat="identity",width=0.45,color="grey",alpha=0.6)+
  scale_x_continuous("Tank",breaks = c(1,2,3,4,5,6,7,8),
                     label=c("RTB-1","RTB-2","RTB-3","RTB-4","RTB-5","RTB-6","RTB-7","RTB-8"))+
  geom_point(data=data,aes(x = Tank, y = data$"Chlorophyll-a (mg/L)"),size=3)+
  geom_point(data=data,aes(x = Tank, y = data$"Chlorophyll-a (mg/L)"),size=6,color="red",alpha=0.2)+
  geom_line(data=data,aes(x = Tank, y = data$"Chlorophyll-a (mg/L)", group=1),color="darkblue",size=1,alpha=0.8)+
  scale_y_continuous(name = expression("Chlorophyll-a (mg/L)"), sec.axis = sec_axis(~ . * 13880000 / 900 , name = "Phytoplankton(cells/L)"))+
  theme(plot.title = element_text(size=14, family = "Times",face="bold"),
        panel.background=element_rect(fill = "snow2"),
        axis.title.x=element_blank(),
        axis.line = element_line(color="grey84", size = 0.5),
        plot.background = element_rect(fill = "snow1"),
        panel.grid.major = element_blank(),
        legend.title = element_blank()) +
  scale_color_brewer(palette="Dark2")

###Method 2
ggplot()+
  geom_bar(data=data2m, aes(x=Tank, y=value*900/13880000 , group=variable, fill=variable),stat="identity",width=0.45,alpha=0.6)+
  scale_fill_brewer(palette="Set3")+
  geom_bar(data=data, aes(x=Tank,y=data$"Phytoplankton(cells/L)"*900/13880000,group=1),stat="identity",width=0.45,color="grey",alpha=0.6, position = position_nudge(x = 0.5))+
  scale_x_continuous("Tank",breaks = c(1.25,2.25,3.25,4.25,5.25,6.25,7.25,8.25),
  label=c("RTB-1","RTB-2","RTB-3","RTB-4","RTB-5","RTB-6","RTB-7","RTB-8"))+
  geom_point(data=data,aes(x = Tank+0.25, y = data$"Chlorophyll-a (mg/L)"),size=3)+
  geom_point(data=data,aes(x = Tank+0.25, y = data$"Chlorophyll-a (mg/L)"),size=6,color="red",alpha=0.2)+
  geom_line(data=data,aes(x = Tank+0.25, y = data$"Chlorophyll-a (mg/L)", group=1),color="darkblue",size=1,alpha=0.8)+
  scale_y_continuous(name = expression("Chlorophyll-a (mg/L)"), sec.axis = sec_axis(~ . * 13880000 / 900 , name = "Phytoplankton(cells/L)"))+
  theme(plot.title = element_text(size=14, family = "Times",face="bold"),
        panel.background=element_rect(fill = "snow2"),
        axis.title.x=element_blank(),
        axis.line = element_line(color="grey84", size = 0.5),
        plot.background = element_rect(fill = "snow1"),
        panel.grid.major = element_blank(),
        legend.title = element_blank()) +
  scale_color_brewer(palette="Dark2")