ggplot常見語法彙總查詢

 

 

主圖

散點圖

柱狀圖

折線圖

小提琴圖

點圖

進化樹

圈圖

Alluvial圖

Sankey Diagram

plot(getSankey(colData(muraro)$cell_type1,  muraro_to_seger$scmap_cluster_labs[,1], plot_height=400))

library(RColorBrewer)
library(scmap)
print(load("-/project/singleCell/mouse/Integration/comp.df.Rdata"))
comp.df$New_cluster <- factor(comp.df$New_cluster, levels = 1:13)
unique(comp.df$New_cluster)

plot(getSankey(comp.df$Old_cluster, comp.df$New_cluster, 
               plot_width=400, plot_height=600, colors=brewer.pal(12,"Set1")))

Marginal plot

library(ggExtra)
#  [density, histogram, boxplot, violin].
ggMarginal(pcag, data=pca_HSCR2, groupColour = T, groupFill=T, size=4, type="boxplot")

Heatmap

• Pheatmap
• ComplexHeatmap Complete Reference

 

 

座標軸

去掉沒必要要的到座標軸的距離，使圖形更加緊湊

ggplot2 Bar Graph remove unnecessary distance between axis label and 0 count on y axis

scale_y_discrete(expand = c(0,0))　　

在對應的座標軸裏用expand來控制

 

座標軸以百分比顯示

scale_y_continuous(labels = percent_format()）

 

x和y軸對角線翻轉

coord_flip()

　　

圖例

圖例的順序翻轉

scale_fill_manual(guide = guide_legend(reverse=F))

　　

分面

 

添加直線

geom_hline(yintercept=0, linetype="dashed", color = "gray30", size=0.1) +
geom_vline(xintercept=6, color = "gray30", size=0.1) +

 

主題

theme_Publication <- function(base_size=11, base_family="helvetica") {
      library(grid)
      library(ggthemes)
      (theme_foundation(base_size=base_size, base_family=base_family)
       + theme(plot.title = element_text(face = "bold",
                                         size = rel(1.2), hjust = 0.5),
               text = element_text(),
               panel.background = element_rect(colour = NA),
               plot.background = element_rect(colour = NA),
               panel.border = element_rect(colour = NA),
               axis.title = element_text(face = "bold",size = rel(1)),
               axis.title.y = element_text(angle=90,vjust =2),
               axis.title.x = element_text(vjust = -0.2),
               axis.text = element_text(), 
               axis.line = element_line(colour="black"),
               axis.ticks = element_line(),
               panel.grid.major = element_line(colour="#f0f0f0"),
               panel.grid.minor = element_blank(),
               legend.key = element_rect(colour = NA),
               legend.position = "bottom",
               legend.direction = "horizontal",
               legend.key.size= unit(0.2, "cm"),
               legend.margin = unit(0, "cm"),
               legend.title = element_text(face="italic"),
               # plot.margin=unit(c(10,5,5,5),"mm"),
               plot.margin=unit(c(5,2,2,2),"mm"),
               strip.background=element_rect(colour="#f0f0f0",fill="#f0f0f0"),
               strip.text = element_text(face="bold")
          ))
      
}

scale_fill_Publication <- function(...){
      library(scales)
      discrete_scale("fill","Publication",manual_pal(values = c("#386cb0","#fdb462","#7fc97f","#ef3b2c","#662506","#a6cee3","#fb9a99","#984ea3","#ffff33")), ...)

}

scale_colour_Publication <- function(...){
      library(scales)
      discrete_scale("colour","Publication",manual_pal(values = c("#386cb0","#fdb462","#7fc97f","#ef3b2c","#662506","#a6cee3","#fb9a99","#984ea3","#ffff33")), ...)

}

　　

 

持續添加~