Barplot bars going the wrong direction [duplicate] - r

Question

This question already has answers here:
Reverse stacked bar order
(2 answers)
Closed 5 years ago.
I'm a biology graduate student learning R. I was hoping someone could help me have the bars go horizontally in the opposite direction (the blue portion should start at 0 and the red at the 100 end of the scale).
Graph with bars in the wrong direction
Here is the data
my_species <- c('apomict_2-17-17_compreh', 'apomict_2-17-17_compreh', 'apomict_2-17-17_compreh', 'apomict_2-17-17_compreh', 'parthenogen_2-17-17_compreh', 'parthenogen_2-17-17_compreh', 'parthenogen_2-17-17_compreh', 'parthenogen_2-17-17_compreh', 'sexual_2-9-17', 'sexual_2-9-17', 'sexual_2-9-17', 'sexual_2-9-17')
my_species <- factor(my_species)
my_species <- factor(my_species,levels(my_species)[c(length(levels(my_species)):1)]) # reorder your species here just by changing the values in the vector :
my_percentage <- c(36.3, 56.3, 2.6, 4.8, 42.2, 50.6, 2.4, 4.8, 56.0, 19.9, 6.7, 17.4)
my_values <- c(522, 811, 38, 69, 608, 729, 35, 68, 806, 286, 96, 252)
category <- c(rep(c("S","D","F","M"),c(1)))
category <-factor(category)
category = factor(category,levels(category)[c(4,1,2,3)])
df = data.frame(my_species,my_percentage,my_values,category)
Here is the code:
# Load the required libraries
library(ggplot2)
library("grid")
# !!! CONFIGURE YOUR PLOT HERE !!!
# Output
#my_output <- paste("/home/loki/","busco_figure.png",sep="/")
my_width <- 20
my_height <- 15
my_unit <- "cm"
# Colors
my_colors <- c("#56B4E9", "#3492C7", "#F0E442", "#F04442")
# Bar height ratio
my_bar_height <- 0.75
# Legend
my_title <- "BUSCO Assessment Results"
# Font
my_family <- "sans"
my_size_ratio <- 1
# Code to produce the graph
labsize = 1
if (length(levels(my_species)) > 10){
labsize = 0.66
}
print("Plotting the figure ...")
figure <- ggplot() +
geom_bar(aes(y = my_percentage, x = my_species, fill = category), data = df, stat="identity", width=my_bar_height) +
coord_flip() +
theme_gray(base_size = 8) +
#scale_y_continuous(labels = c("100","80","60","40","20","0"), breaks = c(100,80,60,40,20,0)) +
scale_y_continuous(labels = c("100","80","60","40","20","0"), breaks = c(100,80,60,40,20,0)) +
#scale_y_continuous(labels = c("100","80","60","40","20","0"), breaks = c(0,20,40,60,80,100)) +
scale_fill_manual(values = my_colors,labels =c(" Complete (C) and single-copy (S) ",
" Complete (C) and duplicated (D)",
" Fragmented (F) ",
" Missing (M)")) +
ggtitle(my_title) +
xlab("") +
ylab("\n%BUSCOs") +
theme(plot.title = element_text(family=my_family, colour = "black", size = rel(2.2)*my_size_ratio, face = "bold")) +
theme(legend.position="top",legend.title = element_blank()) +
theme(legend.text = element_text(family=my_family, size = rel(1.2)*my_size_ratio)) +
theme(panel.background = element_rect(color="#FFFFFF", fill="white")) +
theme(panel.grid.minor = element_blank()) +
theme(panel.grid.major = element_blank()) +
theme(axis.text.y = element_text(family=my_family, colour = "black", size = rel(1.66)*my_size_ratio)) +
theme(axis.text.x = element_text(family=my_family, colour = "black", size = rel(1.66)*my_size_ratio)) +
theme(axis.line = element_line(size=1*my_size_ratio, colour = "black")) +
theme(axis.ticks.length = unit(.85, "cm")) +
theme(axis.ticks.y = element_line(colour="white", size = 0)) +
theme(axis.ticks.x = element_line(colour="#222222")) +
theme(axis.ticks.length = unit(0.4, "cm")) +
theme(axis.title.x = element_text(family=my_family, size=rel(1.2)*my_size_ratio)) +
guides(fill = guide_legend(override.aes = list(colour = NULL))) +
guides(fill=guide_legend(nrow=2,byrow=TRUE))
for(i in rev(c(1:length(levels(my_species))))){
detailed_values <- my_values[my_species==my_species[my_species==levels(my_species)[i]]]
total_buscos <- sum(detailed_values)
figure <- figure +
annotate("text", label=paste("C:", detailed_values[1] + detailed_values[2], " [S:", detailed_values[1], ", D:", detailed_values[2], "], F:", detailed_values[3], ", M:", detailed_values[4], ", n:", total_buscos, sep=""),
y=3, x = i, size = labsize*4*my_size_ratio, colour = "black", hjust=0, family=my_family)
}
my_output="~/temp.png"
ggsave(figure, file=my_output, width = my_width, height = my_height, unit = my_unit)
print("Done")

Answer 1

see ?position_stack:
position_fill() and position_stack() automatically stack values in
reverse order of the group aesthetic, which for bar charts is usually
defined by the fill aesthetic (the default group aesthetic is formed
by the combination of all discrete aesthetics except for x and y).
This default ensures that bar colours align with the default legend.
In order to change the stacking direction, you simply need to add position = position_stack(reverse = TRUE) to geom_bar:
figure <- ggplot() +
geom_bar(
aes(y = my_percentage, x = my_species, fill = category),
data = df, stat="identity", width=my_bar_height,
position = position_stack(reverse = TRUE)) +
coord_flip() +
...
If you don't want to use position_stack, you would have to change factor level and You also have to set filling color breaks to maintain the same legend order.

Answer 2

You need to reorder the factor levels in order for ggplot2 to know what to do. Here is an example of that (note I had to reorder the labels and colors as well):
...
# Colors
my_colors <- c( "#F04442", "#F0E442", "#3492C7", "#56B4E9")
...
df$category = ordered(df$category, levels = c("M", "F", "D", "S"))
figure <- ggplot(data = df[order(df$category, decreasing = F),]) +
geom_bar(aes(y = my_percentage, x = my_species, fill = category), stat="identity", width=my_bar_height) +
coord_flip() +
theme_gray(base_size = 8) +
scale_y_continuous(labels = c("100","80","60","40","20","0"), breaks = c(100,80,60,40,20,0)) +
scale_fill_manual(values = my_colors,labels =c(" Missing (M)",
" Fragmented (F) ",
" Complete (C) and duplicated (D)",
" Complete (C) and single-copy (S) ")) +
...