R语言绘图-Dotplot气泡图

# Dotplot 气泡图
library(tidyverse)
DEG_Dotplot <- function(df, title="") {
  # """
  # data格式如下（需有Description,pvalue,Count,GeneRatio列）
  # !!! 其中GeneRatio必须为数值型，如下图所示，可能需要准换
  # GeneRatio表示点颜色，Count表点的大小，横坐标为p值
  # df表的顺序是什么，画图的顺序就是什么
  #                             Description       pvalue Count GeneRatio
  #GO:0023061                signal release 5.246744e-06    29      0.06
  #GO:0050673 epithelial cell proliferation 6.129368e-06    27      0.06
  #GO:0045444      fat cell differentiation 7.622508e-06    18      0.04
  # resultdir = './result_stringtie/p005fc15'
  # filemark = 'GO_BP_top20_common'
  # 此函数可能需要使用scale_x_continuous调整x轴刻度
  # """
  # 如果已经时数字请删除这二行代码
  df$GeneRatio <- as.numeric(str_split(df$GeneRatio, pattern = '/', simplify = T)[,1])/
                  as.numeric(str_split(df$GeneRatio, pattern = '/', simplify = T)[,2])
  dotplot <- ggplot(cbind(df, Order = nrow(df):1)) +
    geom_point(mapping = aes(x = -log10(pvalue), y = Order, 
                             size = Count, fill = GeneRatio),
               shape = 21) + 
    scale_fill_gradientn(colours = c("grey", "gold", "red")) + #自定义配色
    scale_y_continuous(position = "left", 
                       breaks = 1:nrow(df), 
                       labels = Hmisc::capitalize(rev(df$Description))) +
    #scale_x_continuous(breaks = c(3, 4,5,6),
    #                   #breaks = seq(0, xmax+5, 5),
    #                   limits = c(3,6),
    #                   expand = expansion(mult = c(.05, .05))) + #两边留空
    labs(x = "-Log10(PValue)", y = NULL) +
    guides(size = guide_legend(title = "Gene count"),
           fill = guide_colorbar(title = "GeneRatio")) +
    ggtitle(title) +
    theme_bw() +
    theme(panel.grid =element_blank(),
          panel.grid.major = element_line(color = "gray", linetype = "dashed"),
          panel.border = element_rect(color = "black", linewidth = 1),
          axis.text = element_text(size = 13, family = 'Times'),
          title = element_text(size = 13, family = 'Times')) #去除网格线
  dotplot %>% ggplotGrob()#  %>% cowplot::plot_grid()
  # fname=paste0(resultdir, '/', filemark,'.pdf')
  # ggsave(fname, width = 8, height = 10)
  return(dotplot)
}


# if __name__ == "__main__":
keggdf <- xlsx::read.xlsx("kegg.1.xlsx", sheetIndex = 1)
range(round(-log10(keggdf$pvalue)))
#
p_df <- keggdf[1:15,]
dotplot = DEG_Dotplot(p_df, title="xx")
ggsave(file = "Dotplot_KEGG_top10.pdf", width = 8, height = 7)
#gh <- ggplotGrob(dotplot)
#gd <- ggplotGrob(dotplotk)
#cowplot::plot_grid(gh, gd, rel_widths = c(1.2, 1))