R.ggplot2 - k821209/pipelines GitHub Wiki

칼라 테마들

http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/

library(ggplot2)
data<-read.table('file.Rin',header=F,sep='\t')

Peak annotation

> head(data)
   V1        V2
1 Aly 0.2766870
2 Aly 0.0920515
3 Aly 0.5407250
4 Aly 0.6232970
5 Aly 0.6338910
6 Aly 0.9712740

library(ggplot2)
library(grid)
library(plyr)
densMode <- function(x){
    td <- density(x)
    maxDens <- which.max(td$y)
    list(x=td$x[maxDens], y=td$y[maxDens])
}
xdat <- ddply(data,"V1",transform,val_mean=signif(densMode(V2)$x,3), med.x = signif(densMode(V2)$x,3), med.y=signif(densMode(V2)$y,3))
hp <- ggplot(data=data, aes(x=V2)) +  geom_density() + geom_vline(aes(xintercept=val_mean),xdat, color="red",linetype="dashed",size=1) + theme_bw()
hp<- hp + 
    facet_grid(V1 ~ .) + 
    geom_text(data = xdat, aes(x=med.x,y=med.y,label=val_mean,size=10)) + xlim(0,1)
hp

bar plot

#repeat_stat_ver2.Rin
Copia	31	556	1138	30932	Aly	1.51548848794	0.0322779523166
Solo-LTR	761	4556	408	26932	Aly	11.0257815593	2.86558074588e-322
Gypsy	21	376	1148	31112	Aly	1.51362221069	0.0753685608702
Other	39	768	1130	30720	Aly	1.38053097345	0.0550579190245
Solo-LTR	838	2692	281	23605	Ath	26.1496962134	0.0
Copia	13	129	1106	26168	Ath	2.38434472994	0.00815830574331
Other	10	157	1109	26140	Ath	1.5013238529	0.232988344777
Gypsy	3	33	1116	26264	Ath	2.1394591072	0.180586291765

> df <- read.table('repeat_stat_ver2.Rin',header = FALSE)
> ggplot(df,aes(x=V6,y=-log10(V8),fill=V1)) + geom_bar(stat="identity") + facet_grid(V1 ~ .)

scatter plot

#data
A. lyrata	32657.00	534.00	1169.00
A. thaliana	27416.00	499.00	1119.00
B. rapa	40905.00	637.00	1376.00
C. clementina	24533.00	808.00	2238.00
C. rubella	26521.00	449.00	1022.00
E. grandis	36376.00	2136.00	6509.00
F. vesca	32831.00	453.00	996.00
G. max	56044.00	1131.00	2862.00

> p <- ggplot(df_tandem,aes(x=V4,y=V3,fill=V1,color=V1)) + geom_point(size=4)
> p + geom_text(data= df_tandem, aes(x=V4+400,y=V3,label=V1,size=10)) 
+ theme(legend.text=element_text(size=15,face = "italic")) # SIZE, FONT
+ theme(axis.text.x = element_text(size = rel(2), angle = 00)) # x axis text