CODEWITHSUNDEEP
rggplot2
zahra abdi
zahra abdi

Reputation: 337

How to add the star(s) to my barplot (in ggplot) based on the values in the padj column?

I want to draw a barplot for the data below with the significance level in the padj column.

Here is df:

Genes   CancerType  log2FC  padj
Gene1   Breast  0.230749533 8.01E-07
Gene2   Breast  0.070357349 0.04819805
Gene3   Breast  -0.239713974    0.00059344
Gene4   Breast  0.703365372 5.18E-32
Gene5   Breast  0.327406476 1.01E-12
Gene1   Colon   0.332890058 7.21E-07
Gene2   Colon   0.09527495  0.227845727
Gene3   Colon   -0.178301154    0.196460613
Gene4   Colon   0.924092152 2.70E-16
Gene5   Colon   0.612677767 2.20E-12
Gene1   Lung    0.829893225 5.96E-24
Gene2   Lung    0.2606768   4.57E-05
Gene3   Lung    -0.1821214  0.053233199
Gene4   Lung    0.692721414 4.83E-15
Gene5   Lung    0.688720644 1.83E-27
Gene1   Stomach 0.494758767 1.54E-07
Gene2   Stomach 0.125857219 0.107850978
Gene3   Stomach -0.016071377    0.862073856
Gene4   Stomach 0.203326756 0.094677874
Gene5   Stomach 0.784281834 1.42E-19

And here is the script:

ggplot(data = df, aes(x = CancerType, y = log2FC , fill = Genes)) +
  geom_bar(stat = "identity" , width = 0.7,show.legend = T)+ theme_bw() + facet_wrap(~ Genes)+
  theme(axis.text.x = element_text(size =10, angle = 45, hjust = 1 , colour = "black"))

I don't know how to add the star(s) to each of my barplot based on the values in the padj column.

Thanks for any help.

Upvotes: 0

Views: 345

Answers (1)

Hugo Pineda
Hugo Pineda

Reputation: 51

Here is an option.

You can first create two new columns, one (sig_label) containing the labels based on the padj column and another one, label_position, containing where the label will be place on the y-axis. You can control how far from the bars the labels will be placed by changing the value of nudge.

library(dplyr)
library(ggplot2)
nudge <- 0.075
df |> 
  mutate(
    sig_label = case_when(
      padj < 0.001 ~ "***",
      padj < 0.01 ~ "**",
      padj < 0.05 ~ "*",
      padj >= 0.05 ~ ""
    ),
    label_position = ifelse(log2FC > 0, log2FC + nudge, log2FC - nudge)
  ) |> 
ggplot(aes(x = CancerType, y = log2FC , fill = Genes)) +
  geom_bar(stat = "identity" , width = 0.7,show.legend = T)+ theme_bw() + facet_wrap(~ Genes)+
  theme(axis.text.x = element_text(size =10, angle = 45, hjust = 1 , colour = "black")) +
  geom_text(aes(label = sig_label, y = label_position))

output

Upvotes: 1

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