This repository has been archived by the owner on Jul 30, 2019. It is now read-only.
forked from shendurelab/MAP-C
-
Notifications
You must be signed in to change notification settings - Fork 0
/
MCAST_hits.R
158 lines (141 loc) · 8.49 KB
/
MCAST_hits.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
#
# MCAST_hits.R
#
# Seungsoo Kim
# February 20, 2019
# directories ----
setwd("/Volumes/shendure-vol8/projects/mutagenesis.3C/nobackup/MAP-C")
dir <- "nobackup/mcast"
out <- "figures"
# load libraries
library(ggplot2)
library(dplyr)
library(reshape)
library(RColorBrewer)
library(data.table)
library(grid)
library(gplots)
library(scales)
library(permute)
library(gridExtra)
# colors
brewercols <- brewer.pal(n=6,name="Set1")
classcols <- c(brewercols[2],brewercols[3],brewercols[5])
# homologous motif clusters with all three motifs in S. cer ----
# for Figure 3
for (pthresh in c("0.001")) {
for (mgap in c("200")) {
x <- read.table(paste(dir,"/Scer_",pthresh,"_",mgap,"_Leu3_Sdd4_Rgt1_homologous_LSR.motifs.txt",sep=""))
x <- x[order(x$V13),]
x$V12 <- factor(x$V12,levels=c("Leu3","Sdd4","Rgt1"))
x$genome <- "Scer"
y <- read.table(paste(dir,"/Sbay_",pthresh,"_",mgap,"_Leu3_Sdd4_Rgt1_homologous_LSR.motifs.txt",sep=""))
y <- y[order(y$V13),]
y$V12 <- factor(y$V12,levels=c("Leu3","Sdd4","Rgt1"))
y$genome <- "Suva"
z <- rbind(x,y)
# Figure 3A
pdf(paste(out,"/MCAST_hits_LSR_",pthresh,"_",mgap,".pdf",sep=""),5,0.5*max(z$V7)+1)
print(ggplot(z) + geom_rect(aes(xmin=V8,xmax=V9,ymin=0,ymax=-log10(V13),fill=V12),color="black",size=0.3) +
geom_segment(aes(x=0,xend=V3-V2,y=0,yend=0)) +
facet_grid(V7 ~ genome) + theme_classic() + geom_text(aes(x=max(z$V9)/2,y=8,label=V6),hjust=0.5,size=8*5/14,fontface="italic") +
theme(text=element_text(size=8), axis.text=element_text(size=8,color="black"), legend.text=element_text(size=8,color="black"),
panel.spacing = unit(0.35,"cm"), strip.background = element_blank(),
strip.text = element_blank(),
legend.position = c(0.9,1/(max(z$V7)*2)),legend.background = element_blank(), legend.key.size=unit(0.3,"cm")) +
xlab("") + ylab("") + scale_fill_manual(values=classcols,name="") + scale_y_continuous(breaks=c(0,3,6),limits=c(0,9)))
dev.off()
# Figure 3B
# load ChIP data
chip <- read.table(paste(dir,"/Scer_",pthresh,"_",mgap,"_Leu3_Sdd4_Rgt1_homologous_LSR_maxFE.txt",sep=""))
for (s in c("Leu3","Sdd4","Rgt1")) {
pdf(paste(out,"/MCAST_hits_LSR_ChIP_",s,"_",pthresh,"_",mgap,".pdf",sep=""),0.9,0.5*max(z$V7)+1)
print(ggplot(subset(chip,V4==s)) + geom_bar(aes(x=V5,y=log2(V3),fill=V5),stat="identity",color="black") + facet_wrap(~V2,ncol=1) +
theme_classic() + theme(text=element_text(size=8,color="black"),axis.text=element_text(size=8,color="black"),strip.background = element_blank(),strip.text=element_blank(),legend.position="none") + scale_fill_manual(values=c("grey","red")) + xlab("") + ylab("") +
scale_x_discrete(labels=c("Exp","Sat")) + scale_y_continuous(breaks=scales::pretty_breaks(n=3)))
dev.off()
}
# Figure 3C
# motif clusters ranked by total log2 ChIP enrichment
chip.cast <- cast(subset(chip,V5=="saturated"),V1+V2~V4,value="V3")
chip.cast <- chip.cast[order(-(log2(chip.cast$Leu3)+log2(chip.cast$Sdd4)+log2(chip.cast$Rgt1))),]
chip.cast$rank <- 1:nrow(chip.cast)
pdf(paste(out,"/MCAST_hits_LSR_ChIP_ranked_",pthresh,"_",mgap,".pdf",sep=""),2,2)
print(ggplot(chip.cast) + geom_bar(aes(x=rank,y=log2(Leu3)+log2(Sdd4)+log2(Rgt1)),stat="identity",color="black") +
theme_classic() + theme(text=element_text(size=8,color="black"),
axis.text=element_text(size=8,color="black"),
axis.text.x=element_text(angle=90,vjust=0.5,face="italic"),strip.background = element_blank(),strip.text=element_blank(),legend.position="none") +
xlab("") + ylab("") +
scale_x_continuous(breaks=chip.cast$rank,labels=chip.cast$V1)+
scale_y_continuous(breaks=scales::pretty_breaks(n=3)))
dev.off()
}
}
# all homologous motif clusters ----
# for Figure 3--figure supplement 1
for (pthresh in c("0.001","0.0005")) {
for (mgap in c("50","100","200")) {
x <- read.table(paste(dir,"/Scer_",pthresh,"_",mgap,"_Leu3_Sdd4_Rgt1_homologous.motifs.txt",sep=""))
x <- x[order(x$V13),]
x$V12 <- factor(x$V12,levels=c("Leu3","Sdd4","Rgt1"))
x$genome <- "Scer"
y <- read.table(paste(dir,"/Sbay_",pthresh,"_",mgap,"_Leu3_Sdd4_Rgt1_homologous.motifs.txt",sep=""))
y <- y[order(y$V13),]
y$V12 <- factor(y$V12,levels=c("Leu3","Sdd4","Rgt1"))
y$genome <- "Suva"
z <- rbind(x,y)
# Figure 3--figure supplement 1A
pdf(paste(out,"/MCAST_hits_",pthresh,"_",mgap,".pdf",sep=""),5,0.5*max(z$V7)+1)
print(ggplot(z) + geom_rect(aes(xmin=V8,xmax=V9,ymin=0,ymax=-log10(V13),fill=V12),color="black",size=0.3) +
geom_segment(aes(x=0,xend=V3-V2,y=0,yend=0)) +
facet_grid(V7 ~ genome) + theme_classic() + geom_text(aes(x=max(z$V9)/2,y=8,label=V6),hjust=0.5,size=7*5/14,fontface="italic") +
theme(text=element_text(size=8), axis.text=element_text(size=8,color="black"), legend.text=element_text(size=8,color="black"),
panel.spacing = unit(0.35,"cm"), strip.background = element_blank(),
strip.text = element_blank(),
legend.position = c(0.9,1/(max(z$V7)*2)),legend.background = element_blank(), legend.key.size=unit(0.3,"cm")) +
xlab("") + ylab("") + scale_fill_manual(values=classcols,name="") + scale_y_continuous(breaks=c(0,3,6),limits=c(0,9)))
dev.off()
# Figure 3--figure supplement 1B
# load ChIP data
chip <- read.table(paste(dir,"/Scer_",pthresh,"_",mgap,"_Leu3_Sdd4_Rgt1_homologous_maxFE.txt",sep=""))
for (s in c("Leu3","Sdd4","Rgt1")) {
pdf(paste(out,"/MCAST_hits_ChIP_",s,"_",pthresh,"_",mgap,".pdf",sep=""),0.9,0.5*max(z$V7)+1)
print(ggplot(subset(chip,V4==s)) + geom_bar(aes(x=V5,y=log2(V3),fill=V5),stat="identity",color="black") + facet_wrap(~V2,ncol=1) +
theme_classic() + theme(text=element_text(size=8,color="black"),axis.text=element_text(size=8,color="black"),strip.background = element_blank(),strip.text=element_blank(),legend.position="none") + scale_fill_manual(values=c("grey","red")) + xlab("") + ylab("") +
scale_x_discrete(labels=c("Exp","Sat")) + scale_y_continuous(breaks=scales::pretty_breaks(n=3)))
dev.off()
}
# Figure 3--figure supplement 1C
# motif clusters ranked by total log2 ChIP enrichment
chip.cast <- cast(subset(chip,V5=="saturated"),V1+V2~V4,value="V3")
chip.cast <- chip.cast[order(-(log2(chip.cast$Leu3)+log2(chip.cast$Sdd4)+log2(chip.cast$Rgt1))),]
chip.cast$rank <- 1:nrow(chip.cast)
pdf(paste(out,"/MCAST_hits_ChIP_ranked_",pthresh,"_",mgap,".pdf",sep=""),3.5,1.7)
print(ggplot(chip.cast) + geom_bar(aes(x=rank,y=log2(Leu3)+log2(Sdd4)+log2(Rgt1)),stat="identity",color="black") +
theme_classic() + theme(text=element_text(size=8,color="black"),axis.text=element_text(size=8,color="black"),axis.text.x=element_text(angle=90,vjust=0.5,face="italic"),strip.background = element_blank(),strip.text=element_blank(),legend.position="none") +
xlab("") + ylab("") +
scale_x_continuous(breaks=chip.cast$rank,labels=chip.cast$V1)+
scale_y_continuous(breaks=scales::pretty_breaks(n=3)))
dev.off()
}
}
# all motif clusters in each genome ----
for (genome in c("Scer","Sbay")) {
for (pthresh in c("0.001","0.0005")) {
for (mgap in c("50","100","200")) {
x <- read.table(paste(dir,"/",genome,"_",pthresh,"_",mgap,"_Leu3_Sdd4_Rgt1.motifs.txt",sep=""))
x <- x[order(x$V13),]
x$V12 <- factor(x$V12,levels=c("Leu3","Sdd4","Rgt1"))
pdf(paste(out,"/MCAST_hits_",genome,"_",pthresh,"_",mgap,".pdf",sep=""),2.5,0.5*max(x$V7)+1)
print(ggplot(x) + geom_rect(aes(xmin=V8,xmax=V9,ymin=0,ymax=-log10(V13),fill=V12),color="black",size=0.3) +
geom_segment(aes(x=0,xend=V3-V2,y=0,yend=0)) +
facet_wrap(~V7,ncol=1) + theme_classic() + geom_text(aes(x=max(x$V9)/2,y=8,label=V6),hjust=0.5,size=7*5/14) +
theme(text=element_text(size=8), axis.text=element_text(size=8,color="black"), legend.text=element_text(size=8,color="black"),
panel.spacing = unit(0.35,"cm"), strip.background = element_blank(),
strip.text = element_blank(),
legend.position = c(0.9,0.04),legend.background = element_blank(), legend.key.size=unit(0.3,"cm")) +
xlab("") + ylab("") + scale_fill_manual(values=classcols,name="") + scale_y_continuous(breaks=c(0,3,6),limits=c(0,9)))
dev.off()
}
}
}