project management:

https://mp.weixin.qq.com/s/G-LXN9P2HVLv9v0cvyFJMA

basics on Rstudio

Rstudio常驻小白用户

for (i in 1:length(names)) {

plot.data <- all.data %>% filter(name == i)
p_odd <- ggplot(plot.data) + 
    geom_pointrange(aes(x=factor(cancer.type,levels=cancer.types), y = oddsRatio, 
                        ymin = lowerCI, ymax = upperCI, colour=factor(comparison, levels = names(col_geneList)), 
                        shape= factor(pvalue_shape, levels = p.levels)),
                       position = position_dodge(width = 0.8)) + 
    scale_colour_manual(name = 'Gene.list', values = col_geneList) +
    scale_shape_manual(name = 'P values', values = c("<0.001"=8, "<0.05"=4, ">0.05"=16) ) +   geom_hline(yintercept = 1, linetype = 'dashed', colour = '#bababa') +
    scale_y_continuous(trans = 'log10', limits = c(min_y_lim, max_y_lim),
                       breaks = 10^(ceiling(log10(min_y_lim)):floor(log10(max_y_lim))),
                       labels = sub("0.1", "<0.1", as.character(10^(ceiling(log10(min_y_lim)):floor(log10(max_y_lim))))),
                       expand = c(0.1, 0.1)) +
    xlab('') + ylab('OR') + 
    facet_grid(.~ factor(cancer.type,levels = cancer.types), scales = 'free_x', space = 'free_x') + 
    theme_bw() + theme_hz +
    theme(axis.text.x = element_text(angle = 90, vjust = 0.5), 
          panel.background = element_rect(fill = '#fde0ef50'), 
          panel.grid = element_blank(),
          strip.background = element_blank(), strip.text.x = element_blank())
  p_odd

pdf(paste(dir,'odd_', i, '.pdf'), width = 8, height = 5)
print(p_odd)
dev.off()

}