how to add the p value onto basic ggplots.
see reference: https://www.datanovia.com/en/blog/how-to-add-p-values-onto-basic-ggplots/
library(Jerry)
#> Loading required package: tidyverse
#> Warning: package 'tidyverse' was built under R version 4.0.5
#> -- Attaching packages --------------------------------------- tidyverse 1.3.1 --
#> v ggplot2 3.3.3 v purrr 0.3.4
#> v tibble 3.1.1 v dplyr 1.0.6
#> v tidyr 1.1.3 v stringr 1.4.0
#> v readr 1.4.0 v forcats 0.5.1
#> Warning: package 'ggplot2' was built under R version 4.0.5
#> Warning: package 'tibble' was built under R version 4.0.5
#> Warning: package 'tidyr' was built under R version 4.0.5
#> Warning: package 'readr' was built under R version 4.0.3
#> Warning: package 'forcats' was built under R version 4.0.5
#> -- Conflicts ------------------------------------------ tidyverse_conflicts() --
#> x dplyr::filter() masks stats::filter()
#> x dplyr::lag() masks stats::lag()
#> Warning: replacing previous import 'ggplot2::annotate' by 'ggpmisc::annotate'
#> when loading 'Jerry'
library(ggpubr)
library(rstatix)
#>
#> Attaching package: 'rstatix'
#> The following object is masked from 'package:stats':
#>
#> filter
data(signatures)
head(signatures)
#> Tumor_Sample_Barcode Signature.1 Signature.6 Signature.17 Signature.15
#> 1 M01_1D_Aca 0.000000 3.660088 0.0000000 0.000000
#> 2 M03_1A_Aca 57.638866 0.000000 1.3355527 20.316812
#> 3 M03_1B_Aca 44.026712 3.300601 0.0000000 18.114416
#> 4 M03_1C_Aca 43.686315 15.573550 0.2367439 4.903536
#> 5 M03_1D_Aca 55.881582 15.169653 0.3350532 11.077736
#> 6 M04_11H_Aca 9.724408 0.000000 0.0000000 6.571080
#> Signature.3 mutNum sig6 group
#> 1 9.20233 13 noS6 Aca.early
#> 2 0.00000 74 noS6 Aca.early
#> 3 0.00000 62 noS6 Aca.early
#> 4 0.00000 64 S6 Aca.early
#> 5 0.00000 80 S6 Aca.early
#> 6 33.81792 51 noS6 Aca.early
#non-params test: wilcox_test
wilcox.test = signatures %>%
group_by(group) %>%
wilcox_test(mutNum ~ sig6) %>%
add_xy_position(x = "sig6", fun = "mean_sd" ) %>%
add_significance("p")
signatures %>%
ggboxplot(
x = "sig6", y = "mutNum", col = "sig6",
facet.by = "group", scales = "free",
xlab = "signature 6", ylab = "# muts",
add = "jitter", add.params = list(width = 0.1, size = 1, shape = 1) ,
ggtheme = theme_classic()) +
stat_pvalue_manual(wilcox.test, label = "p") +
guides(color = "none" )
signatures %>%
ggboxplot(
x = "sig6", y = "mutNum", col = "sig6",
facet.by = "group", scales = "free",
xlab = "signature 6", ylab = "# muts",
add = "jitter", add.params = list(width = 0.1, size = 1, shape = 1) ,
ggtheme = theme_classic()) +
stat_pvalue_manual(wilcox.test, label = "p.signif") +
guides(color = "none" )