Hi, I have this dataframe from RNAseq enrichment pathways : 4 columns (Module, Pathway, OR, adjusted p=value) and 83 rows (enriched pathways)
Module Pathway OR Adjusted p-value
Gene_atlas WholeBlood 9.035869654 0.005206627
Gene_atlas CD14+_Monocytes 3.610643472 0.036066265
GO_Biological Process GO:0045321_leukocyte activation 4.316600829 0.003847901
I have plot this data with ggplot2. This is my R code :
gplot(my_data_C2C1, aes(x = reorder(Pathway, Adjusted.p.value), y = -log10(Adjusted.p.value), fill = Module)) + geom_bar(stat = "identity")
But I do no see correctly my pathway names. So, I would like to flip my data :
ggplot(my_data_C2C1, aes(x = reorder(Pathway, Adjusted.p.value), y = -log10(Adjusted.p.value), fill = Module)) + geom_bar(stat = "identity") + coord_flip()
I see better the pathway names but no totally and the bars have disapeared.
How can I reduce the police size of my pathway names and display the bars ?
Thans a lot for your help,
Best,
Jessica
•
written
by
garciajessica0311 •
Does converting the underscores to new-lines help?
my_data_C2C1$Pathway <- gsub("_","\n",my_data_C2C1$Pathway)
The example dataset in your post works fine for both scripts - if you can't see the bars you probably need to make the display window larger.
Yes, the windows was too small ... Sorry ! Many thanks for your help ! It's perfect
We can use the str_wrap( ) function from stringr package to process the text, here is a example on scale_x_discrete(). we can also apply this function to other text content.
# R code
library(ggplot2) # version 3.3.0
library(stringr) # version 1.4.0
library(patchwork) # version 1.0.0
### demo data
df <- data.frame(name = "wrap the text by fix width", score = 1)
### wrap the text
p1 <- ggplot(df, aes(name, score)) +
geom_bar(stat = "identity")
p2 <- ggplot(df, aes(name, score)) +
geom_bar(stat = "identity") +
scale_x_discrete(labels = function(x) str_wrap(x, width = 15))
p1 + p2
a new feature added in ggplot2 version 3.3.0 , Bi-directional geoms, so we can achieve the same goal as coord_flip() by specify aes(x = score, y = name), here are the code:
See ggplot2 new features link
### switch the coordinates
p1 <- ggplot(df, aes(score, name)) +
geom_bar(stat = "identity")
p2 <- ggplot(df, aes(score, name)) +
geom_bar(stat = "identity") +
scale_y_discrete(labels = function(x) str_wrap(x, width = 15))
p1 + p2
Thanks for your help ! I keep in mind this technic
In addition to the line breaks, you can also change the angle of the labels (e.g. to 90 degrees) and the size of the labels as explained in the R cookbook.
Log in to answer this question.
