色彩 | 单细胞漂亮的配色效果

1. DotPlot

主要参数：scale_color_gradientn(values = seq(0,1,0.2),colours = c(‘#330066’,‘#336699’,‘#66CC66’,‘#FFCC33’))

DotPlot(combined.obj, features = c('CD3D','CD3E','CD3G','GNLY','NKG7',
                         'CD79A','CD79B','MZB1',"TNFRSF17",
                         'CD14','CD163','CD68','FCGR3A',"MPO","ELANE",
                         'CLEC10A','CD1C',"LILRA4","CLEC4C",
                         'PPBP','PF4'))+
  coord_flip()+
  theme_bw(base_size = 14)+  
  theme(panel.grid = element_blank())+ 
  scale_color_gradientn(values = seq(0,1,0.2),colours = c('#330066','#336699','#66CC66','#FFCC33'))+  
  labs(x=NULL,y=NULL)+guides(size=guide_legend(order=3))

2. Seurat 自带的四个调色板

• 见 Seurat 4 R包源码解析 24: step11 降维可视化 DimPlot() 3(9)

默认根据颜色数量挑选调色板，不过可以自己指定。

这里同时给出具体颜色值。

# palette 
#alphabet  alphabet2    glasbey polychrome    stepped 
#      26         26         32         36         24 

pname=c('alphabet', 'alphabet2', 'glasbey', 'polychrome', 'stepped')
nArr=c(26, 26, 32, 36, 24)
par(mfrow=c(5,1), mar=c(0,0,1.5,0))
for(i in 1:5 ){
  title=sprintf( "%s(n=%s)", pname[i], nArr[i] )
  message(i, " | ", title)
  colors=Seurat::DiscretePalette(n=nArr[i], pname[i])
  barplot( rep(1, length(colors)), col=colors, main=title,
           yaxt='n', space=0, border = NA )
}

(1) alphabet | 26

> DiscretePalette(26, palette='alphabet')
 [1] "#F0A0FF" "#0075DC" "#993F00" "#4C005C" "#191919" "#005C31" "#2BCE48"
 [8] "#FFCC99" "#808080" "#94FFB5" "#8F7C00" "#9DCC00" "#C20088" "#003380"
[15] "#FFA405" "#FFA8BB" "#426600" "#FF0010" "#5EF1F2" "#00998F" "#E0FF66"
[22] "#740AFF" "#990000" "#FFFF80" "#FFE100" "#FF5005"
> DiscretePalette(26, palette='alphabet') |> scales::show_col()
> mtext("alphabet", side=3, line=3, cex=1, col="forestgreen")

(2) alphabet2 | 26

> colName="alphabet2"
> DiscretePalette(26, palette=colName)
 [1] "#AA0DFE" "#3283FE" "#85660D" "#782AB6" "#565656" "#1C8356" "#16FF32"
 [8] "#F7E1A0" "#E2E2E2" "#1CBE4F" "#C4451C" "#DEA0FD" "#FE00FA" "#325A9B"
[15] "#FEAF16" "#F8A19F" "#90AD1C" "#F6222E" "#1CFFCE" "#2ED9FF" "#B10DA1"
[22] "#C075A6" "#FC1CBF" "#B00068" "#FBE426" "#FA0087"
> DiscretePalette(26, palette=colName) |> scales::show_col()
> mtext(colName, side=3, line=3, cex=1, col="forestgreen")

(3) glasbey | 32

> colName="glasbey"
> DiscretePalette(32, palette=colName)
 [1] "#0000FF" "#FF0000" "#00FF00" "#000033" "#FF00B6" "#005300" "#FFD300"
 [8] "#009FFF" "#9A4D42" "#00FFBE" "#783FC1" "#1F9698" "#FFACFD" "#B1CC71"
[15] "#F1085C" "#FE8F42" "#DD00FF" "#201A01" "#720055" "#766C95" "#02AD24"
[22] "#C8FF00" "#886C00" "#FFB79F" "#858567" "#A10300" "#14F9FF" "#00479E"
[29] "#DC5E93" "#93D4FF" "#004CFF" "#F2F318"
> DiscretePalette(32, palette=colName) |> scales::show_col()
> mtext(colName, side=3, line=3, cex=1, col="forestgreen")

(4) polychrome | 36

> colName="polychrome"
> DiscretePalette(36, palette=colName)
 [1] "#5A5156" "#E4E1E3" "#F6222E" "#FE00FA" "#16FF32" "#3283FE" "#FEAF16"
 [8] "#B00068" "#1CFFCE" "#90AD1C" "#2ED9FF" "#DEA0FD" "#AA0DFE" "#F8A19F"
[15] "#325A9B" "#C4451C" "#1C8356" "#85660D" "#B10DA1" "#FBE426" "#1CBE4F"
[22] "#FA0087" "#FC1CBF" "#F7E1A0" "#C075A6" "#782AB6" "#AAF400" "#BDCDFF"
[29] "#822E1C" "#B5EFB5" "#7ED7D1" "#1C7F93" "#D85FF7" "#683B79" "#66B0FF"
[36] "#3B00FB"
> DiscretePalette(36, palette=colName) |> scales::show_col()
> mtext(colName, side=3, line=3, cex=1, col="forestgreen")

(6) stepped | 24

> colName="stepped"
> DiscretePalette(24, palette=colName)
 [1] "#990F26" "#B33E52" "#CC7A88" "#E6B8BF" "#99600F" "#B3823E" "#CCAA7A"
 [8] "#E6D2B8" "#54990F" "#78B33E" "#A3CC7A" "#CFE6B8" "#0F8299" "#3E9FB3"
[15] "#7ABECC" "#B8DEE6" "#3D0F99" "#653EB3" "#967ACC" "#C7B8E6" "#333333"
[22] "#666666" "#999999" "#CCCCCC"
> DiscretePalette(24, palette=colName) |> scales::show_col()
> mtext(colName, side=3, line=3, cex=1, col="forestgreen")

Ref:

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