Hi all,
The words in the x axis are too small to read, so I try to increase by use size = 20. However the x axis didn't change size regardless of input in size and it is not bold:
ggplot(data, aes(x = Pathway, y = Beta, fill = Genotype)) +
geom_bar(stat = "identity", position = position_dodge()) +
theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 20, face = "bold"))
Would you please have a suggestion? I appreciate it!
ggplot(mtcars, aes(x = rownames(mtcars), y = mpg, fill = cyl)) +
geom_bar(stat = "identity", position = position_dodge()) +
theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 20, face = "bold"))
Your code works for me (I just modified it to plotting sample data). Which plotting device do you use and which version of ggplot? Does the 45-degree rotation work?
Hi Matt, angle 45 didn't work. ggplot2 3.5.1. I just plot in Rstudio.
data <- data.frame(
Pathway = c("BIOCARTA_IL12_PATHWAY", "CONRAD_STEM_CELL"),
group1 = c(0.027233015, -0.025555915),
group2 = c(-0.01753847, 0.01116901)
)
data <- melt(data, id.vars = "Pathway", variable.name = "Genotype", value.name = "Beta")
If the angle45 also didn't work, then there is something odd with the plotting device, either a missing library like Cairo or maybe a lack of permissions. You can try reading through library(help = "grDevices") to learn more and change the plotting device. Which plotting device is the default depends on your OS, but the first thing to try would be switching that temporarily.
myplot <- ggplot(mtcars, aes(x = rownames(mtcars), y = mpg, fill = cyl)) +
geom_bar(stat = "identity", position = position_dodge()) +
theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 20, face = "bold"))
png("Test-cairo.png",type="cairo")
myplot
dev.off()
png("Test-xlib.png",type="Xlib")
myplot
dev.off()
png("Test-quarz.png",type="quarz")
myplot
dev.off()
A quick reference for the different devices is usually available with ?png, ?tiff, ?pdf, ?svg etc. I suspect particularly an issue with the vector devices and the fonts.
I really don't see why that should depend on the data being plotted. But I nonetheless tried, and the formatting was applied as well.
Sorry, but I can't help you beyond the dreaded "Works for me / on my machine". If you have e.g. Docker or Singularity, you could try the containerized version of Tidyverse just to double-check that it is not a problem with the Graphics Device.
PS: mind that melt is superseded by pivot_longer in the meantime.
I got this result. Didn't you?
data <- data.frame(
Pathway = c("BIOCARTA_IL12_PATHWAY", "CONRAD_STEM_CELL"),
group1 = c(0.027233015, -0.025555915),
group2 = c(-0.01753847, 0.01116901)
)
data <- melt(data, id.vars = "Pathway", variable.name = "Genotype", value.name = "Beta")
#Warning message:
#The melt generic in data.table has been passed a data.frame and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is #superseded and is no longer actively developed, and this redirection is now deprecated. To continue using melt methods from reshape2 while both libraries #are attached, e.g. melt.list, you can prepend the namespace, i.e. reshape2::melt(data). In the next version, this warning will become an error.
data
Pathway Genotype Beta
1 BIOCARTA_IL12_PATHWAY group1 0.02723301
2 CONRAD_STEM_CELL group1 -0.02555591
3 BIOCARTA_IL12_PATHWAY group2 -0.01753847
4 CONRAD_STEM_CELL group2 0.01116901
ggplot(data, aes(x = Pathway, y = Beta, fill = Genotype)) +
geom_bar(stat = "identity", position = position_dodge()) +
theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 20, face = "bold"))
It turns out the reason is because:
ggplot(data_melted, aes(x = Pathway, y = Beta, fill = Genotype)) +
geom_bar(stat = "identity", position = position_dodge()) +
theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 4, face = "bold")) +
labs(title = "Comparison of Beta Values Between group 1 and group 2",
x = "Pathway",
y = "Beta Value",
fill = "Genotype") +
theme_minimal() + theme(plot.title = element_text(hjust = 0.5))+
scale_fill_manual(values = c("group1" = "green", "group2" = "red"))
I thought the extra modification can't cause the issue but it is. So how can I still increase font size when using extra modification like this? Thank you.
Update. The conflict in theme cause the issue. I figure it out. Thank you.
Do not use theme() function twice. The following code will give you the result you wanted.
ggplot(data_melted, aes(x = Pathway, y = Beta, fill = Genotype)) +
geom_bar(stat = "identity", position = position_dodge()) +
labs(title = "Comparison of Beta Values Between group 1 and group 2",
x = "Pathway",
y = "Beta Value",
fill = "Genotype") +
theme_minimal() +
scale_fill_manual(values = c("group1" = "green", "group2" = "red"))+theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 8, face = "bold"), plot.title = element_text(hjust = 0.5))
Technically, you can use theme() as often as you want, but the order matters. Contrary to math, where a + b = b + a applies, ggplot2 plots are built up in a layered fashion.
Starting from the base plot, you apply additional geometries or selective theme modifications with increasing specificity. Adding theme_minimal() after your desired modification was resetting all prior theme attributes, because it is a complete theme that comprises style settings for each element.
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