R作图配色问题

1. R自带颜色

image.png

2. RColorBrewer

library(RColorBrewer)
?RColorBrewer

brewer.pal(n, name)
display.brewer.pal(n, name)
display.brewer.all(n=NULL, type="all", select=NULL, exact.n=TRUE,
colorblindFriendly=FALSE)
brewer.pal.info

Accent 8
Dark2 8
Paired 12
Pastel1 9
Pastel2 8
Set1 9
Set2 8
Set3 12

display.brewer.pal(11,"PiYG")
display.brewer.pal(4,"PiYG")
display.brewer.pal(9, "Set1")
display.brewer.pal(9, "Set2")
display.brewer.pal(11,"Pastel1")
display.brewer.pal(4,"Pastel2") display.brewer.pal(9, "Paired")

for example

mycols<-c(brewer.pal(9, "Paired"))
p <- DimPlot(sce, reduction = 'tsne',  label = TRUE, pt.size = 0.5,raster=FALSE,cols=mycols)
p

image.png

3. ggsci

library("ggsci")

For all the color palettes, the corresponding scales are named as:

scale_color_palname()
scale_fill_palname()

1. NPG  scale_color_npg()      scale_fill_npg()     "nrc"   pal_npg()
2. AAAS scale_color_aaas()    scale_fill_aaas() "default"   pal_aaas()
3. NEJM scale_color_nejm()    scale_fill_nejm() "default"   pal_nejm()
4. Lancet   scale_color_lancet()  scale_fill_lancet()   "lanonc"    pal_lancet()
5. JAMA 
JCO
UCSCGB  
D3  
LocusZoom
IGV 
UChicago    
Star Trek   scale_color_startrek() 
Tron Legacy scale_color_tron()
Futurama    
Rick and Morty  scale_color_rickandmorty()
The Simpsons    scale_color_simpsons() 
GSEA    
Material Design scale_color_material() 

for example

p <- DimPlot(sce, reduction = 'tsne',  label = TRUE, pt.size = 0.5,raster=FALSE)
p +scale_color_npg()

image.png

4. 图片保存常用方法

library(ggpubr)
g<-ggexport(plotlist = list(a,p), filename = "clusters.pdf")