How to add axis text in this negative and positive bars differently using ggplot2?

Question

I've drawed bar graph with negative and positive bars which is familiar to the research. However, my code seems extremely inconvenient and verbose usinggraphics::plot() and graphics::text() as showed below. Try as I may, I could find the solution using element_text to fulfill in ggplot2. Please help or try to give some ideas how to achieve this in ggplot2.Thanks in advance.

# my data
df <- data.frame(genus=c("Prevotella","Streptococcus","YRC22","Phascolarctobacterium","SMB53","Epulopiscium",
                         "CF231","Anaerovibrio","Paludibacter","Parabacteroides","Desulfovibrio","Sutterella",
                         "Roseburia","Others__0_5_","Akkermansia","Bifidobacterium","Campylobacter","Fibrobacter",
                         "Coprobacillus","Bulleidia","f_02d06","Dorea","Blautia","Enterococcus","Eubacterium",
                         "p_75_a5","Clostridium","Coprococcus","Oscillospira","Escherichia","Lactobacillus"),
                 class=c(rep("groupA",18),rep("groupB",13)),
                 value=c(4.497311,4.082377,3.578472,3.567310,3.410453,3.390026,
                         3.363542,3.354532,3.335634,3.284165,3.280838,3.218053,
                         3.071454,3.026663,3.021749,3.004152,2.917656,2.811455,
                        -2.997631,-3.074314,-3.117659,-3.151276,-3.170631,-3.194323,
                        -3.225207,-3.274281,-3.299712,-3.299875,-3.689051,-3.692055,
                        -4.733154)
     )

# bar graph 
tiff(file="lefse.tiff",width=2000,height=2000,res=400)
par(mar=c(5,2,1,1))
barplot(df[,3],horiz=T,xlim=c(-6,6),xlab="LDA score (log 10)",
        col=c(rep("forestgreen",length(which(df[,2]=="groupA"))),
              rep("goldenrod",length(which(df[,2]=="groupB")))))
axis(1,at=seq(-6,6,by=1))
# add text
text(0.85,36.7,label=df[,1][31],cex=0.6);text(0.75,35.4,label=df[,1][30],cex=0.6)
text(0.75,34.1,label=df[,1][29],cex=0.6);text(0.85,33.0,label=df[,1][28],cex=0.6)
text(0.75,31.8,label=df[,1][27],cex=0.6);text(0.6,30.6,label=df[,1][26],cex=0.6)
text(0.8,29.5,label=df[,1][25],cex=0.6);text(0.85,28.3,label=df[,1][24],cex=0.6)
text(0.45,27.1,label=df[,1][23],cex=0.6);text(0.4,25.9,label=df[,1][22],cex=0.6)
text(0.55,24.7,label=df[,1][21],cex=0.6);text(0.55,23.5,label=df[,1][20],cex=0.6)
text(0.85,22.3,label=df[,1][19],cex=0.6);text(-0.75,21.1,label=df[,1][18],cex=0.6)
text(-1,19.9,label=df[,1][17],cex=0.6);text(-1,18.8,label=df[,1][16],cex=0.6)
text(-0.85,17.6,label=df[,1][15],cex=0.6);text(-0.85,16.3,label=df[,1][14],cex=0.6)
text(-0.7,15.1,label=df[,1][13],cex=0.6);text(-0.65,13.9,label=df[,1][12],cex=0.6)
text(-0.85,12.7,label=df[,1][11],cex=0.6);text(-1.05,11.5,label=df[,1][10],cex=0.6)
text(-0.85,10.3,label=df[,1][9],cex=0.6);text(-0.85,9.1,label=df[,1][8],cex=0.6)
text(-0.47,7.9,label=df[,1][7],cex=0.6);text(-0.85,6.7,label=df[,1][6],cex=0.6)
text(-0.49,5.5,label=df[,1][5],cex=0.6);text(-1.44,4.3,label=df[,1][4],cex=0.6)
text(-0.49,3.1,label=df[,1][3],cex=0.6);text(-0.93,1.9,label=df[,1][2],cex=0.6)
text(-0.69,0.7,label=df[,1][1],cex=0.6)
# add lines
segments(0,-1,0,40,lty=3,col="grey")
segments(2,-1,2,40,lty=3,col="grey")
segments(4,-1,4,40,lty=3,col="grey")
segments(6,-1,6,40,lty=3,col="grey")
segments(4,-1,4,40,lty=3,col="grey")
segments(-2,-1,-2,40,lty=3,col="grey")
segments(-4,-1,-4,40,lty=3,col="grey")
segments(-6,-1,-6,40,lty=3,col="grey")
legend("topleft",bty="n",cex=0.65,inset=c(0.01,-0.02),ncol=2,
       legend=c("groupA","groupB"),
       col=c("forestgreen", "goldenrod"),pch=c(15,15))
dev.off()

Answer 1

Here's a solution using dplyr to create some extra columns for the label position and the justification, and then theming the plot to match reasonably closely what you originally had:

library("dplyr")
library("ggplot2")
df <- df %>%
  mutate(
    genus = factor(genus, levels = genus[order(value, decreasing = TRUE)]),
    label_y = ifelse(value < 0, 0.2, -0.2),
    label_hjust = ifelse(value < 0, 0, 1)
  )

my_plot <- ggplot(df, aes(x = genus, y = value, fill = class)) +
  geom_bar(stat = "identity", col = "black") +
  geom_text(aes(y = label_y, label = genus, hjust = label_hjust)) +
  coord_flip() +
  scale_fill_manual(values = c(groupA = "forestgreen", groupB = "goldenrod")) +
  theme_minimal() +
  theme(axis.text.y = element_blank(),
        axis.ticks.y = element_blank(),
        axis.title.y = element_blank(),
        legend.position = "top",
        legend.justification = 0.05,
        legend.title = element_blank(),
        panel.grid.major.y = element_blank(),
        panel.grid.minor.y = element_blank(),
        panel.grid.major.x = element_line(colour = "grey80", linetype = "dashed"),
        panel.grid.minor.x = element_blank()) +
  scale_y_continuous(expression(log[10](italic("LDA score"))),
                     breaks = -6:6, limits = c(-6, 6))

print(my_plot)
ggsave("lefse.tiff", width = 5, height = 5, dpi = 400, my_plot)

Answer 2

I would try this:

library(ggplot2)

# change the factor levels so it will be displayed in correct order
df$genus <- factor(df$genus, levels = as.character(df$genus))

ggplot(df, aes(x = genus, y = value)) +
    geom_bar(aes(fill = class), stat = 'identity') +  # color by class
    coord_flip() +  # horizontal bars
    geom_text(aes(y = 0, label = genus, hjust = as.numeric(value > 0))) +  # label text based on value
    theme(axis.text.y = element_blank())

In the above, hjust will change the direction of the text relative to its y position (flipped to x now), which is similar to pos parameter in base R plot. So you code could also be simplified with a vector for pos argument to text function.

Answer 3

Two options:

library(ggplot2)

# my data
df <- data.frame(genus=c("Prevotella","Streptococcus","YRC22","Phascolarctobacterium","SMB53","Epulopiscium",
                         "CF231","Anaerovibrio","Paludibacter","Parabacteroides","Desulfovibrio","Sutterella",
                         "Roseburia","Others__0_5_","Akkermansia","Bifidobacterium","Campylobacter","Fibrobacter",
                         "Coprobacillus","Bulleidia","f_02d06","Dorea","Blautia","Enterococcus","Eubacterium",
                         "p_75_a5","Clostridium","Coprococcus","Oscillospira","Escherichia","Lactobacillus"),
                 class=c(rep("groupA",18),rep("groupB",13)),
                 value=c(4.497311,4.082377,3.578472,3.567310,3.410453,3.390026,
                         3.363542,3.354532,3.335634,3.284165,3.280838,3.218053,
                         3.071454,3.026663,3.021749,3.004152,2.917656,2.811455,
                         -2.997631,-3.074314,-3.117659,-3.151276,-3.170631,-3.194323,
                         -3.225207,-3.274281,-3.299712,-3.299875,-3.689051,-3.692055,
                         -4.733154)
)

ggplot(df, aes(reorder(genus, -value), value, fill = class)) +
    geom_bar(stat = "identity") +
    coord_flip() +
    geom_text(aes(label = genus,
                  y = ifelse(value < 1, 1.5, -1.5)), size = 2.5) +
    theme(axis.title.y=element_blank(),
          axis.text.y=element_blank(),
          axis.ticks.y=element_blank())

Or this:

library(ggplot2)

# my data
df <- data.frame(genus=c("Prevotella","Streptococcus","YRC22","Phascolarctobacterium","SMB53","Epulopiscium",
                         "CF231","Anaerovibrio","Paludibacter","Parabacteroides","Desulfovibrio","Sutterella",
                         "Roseburia","Others__0_5_","Akkermansia","Bifidobacterium","Campylobacter","Fibrobacter",
                         "Coprobacillus","Bulleidia","f_02d06","Dorea","Blautia","Enterococcus","Eubacterium",
                         "p_75_a5","Clostridium","Coprococcus","Oscillospira","Escherichia","Lactobacillus"),
                 class=c(rep("groupA",18),rep("groupB",13)),
                 value=c(4.497311,4.082377,3.578472,3.567310,3.410453,3.390026,
                         3.363542,3.354532,3.335634,3.284165,3.280838,3.218053,
                         3.071454,3.026663,3.021749,3.004152,2.917656,2.811455,
                         -2.997631,-3.074314,-3.117659,-3.151276,-3.170631,-3.194323,
                         -3.225207,-3.274281,-3.299712,-3.299875,-3.689051,-3.692055,
                         -4.733154)
)

ggplot(df, aes(reorder(genus, -value), value, fill = class)) +
    geom_bar(stat = "identity") +
    coord_flip() +
    xlab("genus")