Import relevant library (ggplot2)

Install ggplot2 with install.packages before importing for plotting purposes below.

#install.package("ggplot2")
library(ggplot2)

path = '/home/genewalk/qki/'
filename = 'genewalk_results.csv' 

Load GeneWalk results file

GW = read.csv(paste(path,filename,sep=""),header = TRUE)

GW$mlog10padj = -log10(GW$gene_padj) #calculate -log10 values
GW$mlog10padj_err = -log10(GW$cilow_gene_padj) - GW$mlog10padj #calculate -log10 error bars

Plot GeneWalk annotation relevance scores bar charts

alpha_FDR_plot = 0.05
GENES = c('MAL','PLP1')

for (gene in GENES){
  
  dplot = GW[which(GW$hgnc_symbol==gene),]    
  #for plotting: order GO terms according to gene_padj (and if equal then sort by cosine similarity)
  dplot$go_name = factor(dplot$go_name, 
                         levels = dplot$go_name[with(dplot,order(-gene_padj,sim))])
  
  font_sz=12
  ymax=max(dplot$mlog10padj + dplot$mlog10padj_err) + 0.3
  
  f = ggplot(dplot, aes(go_name,mlog10padj)) + 
  theme_light(base_size=font_sz) +
  geom_bar(stat='identity',fill='royalblue',width=0.8) +
  geom_errorbar(aes(ymin=mlog10padj-mlog10padj_err, ymax=mlog10padj+mlog10padj_err),
                width=0.2, color='grey') +
  geom_hline(yintercept=-log10(alpha_FDR_plot), color='red', linetype='dashed') +
  xlab('') +
  ylab('-log10(gene p-adjust)') +
  theme(panel.grid.major.y = element_blank(),
        panel.grid.minor.y = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.ticks = element_blank(),
        axis.title.x = element_text(size=font_sz*0.8)) +
  scale_y_continuous(breaks=c(0,1,2,3,4),
                     limits = c(0, ymax)) +
  coord_flip()+
  ggtitle(gene)
  
  #f   
  
  gonames = as.character(dplot$go_name)
  lchar = sapply(gonames, nchar)
  w0 = max(lchar)
  
  fname = paste('barplot_',gene,'_x_mlog10gene_padj_y_GO.',sep="") 
  ggsave(paste(path,fname,'pdf',sep=""),
         f,
         width = (ymax*0.3+w0*0.1),
         height=(0.2+0.25*length(dplot$go_name)))#units:inch
  ggsave(paste(path,fname,'png',sep=""),
         f,
         width = (ymax*0.3+w0*0.1),
         height=(0.2+0.25*length(dplot$go_name)))
}

SessionInfo

sessionInfo()

## R version 3.5.0 (2018-04-23)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS High Sierra 10.13.6
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] ggplot2_3.3.2
## 
## loaded via a namespace (and not attached):
##  [1] knitr_1.30       magrittr_1.5     tidyselect_1.1.0 munsell_0.5.0   
##  [5] colorspace_1.4-1 R6_2.4.1         rlang_0.4.8      stringr_1.4.0   
##  [9] dplyr_1.0.2      tools_3.5.0      grid_3.5.0       gtable_0.3.0    
## [13] xfun_0.18        withr_2.3.0      htmltools_0.5.0  ellipsis_0.3.1  
## [17] yaml_2.2.1       digest_0.6.26    tibble_3.0.4     lifecycle_0.2.0 
## [21] crayon_1.3.4     farver_2.0.3     purrr_0.3.4      vctrs_0.3.4     
## [25] glue_1.4.2       evaluate_0.14    rmarkdown_2.5    stringi_1.5.3   
## [29] compiler_3.5.0   pillar_1.4.6     generics_0.0.2   scales_1.1.1    
## [33] pkgconfig_2.0.3