-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathpolarise_plot_AFs.R
277 lines (206 loc) · 8.41 KB
/
polarise_plot_AFs.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
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
# new general run
rm(list=ls()) #clears all variables
objects() # clear all objects
graphics.off() #close all figures
lib<-as.vector(c("ggplot2","dplyr","tidyr","stringr","data.table","plyr","viridis"))
lapply(lib,library,character.only=TRUE)
## working directory
setwd("~/Dropbox/Sussex_Guppies/Analyses/pool-seq/geno_plots/")
#########################################
## LG1 plot ##
#########################################
## read in the frequencies
chr1 <- data.frame(fread("~/Dropbox/Sussex_Guppies/Analyses/pool-seq/poolfstat/outputs/final/chr1_AFs_final.tsv", header=TRUE))
## Polarise to IF9:
## remove pos
tmp <- chr1 %>% dplyr::select(IF10_AF, IF6_AF, IF8_AF, IF9_AF)
## save the IF9 freqs:
IF9_freqs<-tmp$IF9_AF
# Polarise to IF9
for(i in colnames(tmp)){
tmp[IF9_freqs < 0.5,i]<-(1-tmp[IF9_freqs < 0.5,i])
}
## add IF9 polarised back in back in:
chr1_dd <- cbind(chr1,tmp)
colnames(chr1_dd) <- c("chr", "pos", "REF", "ALT", "IF10_AF", "IF6_AF", "IF8_AF", "IF9_AF",
"IF10_polar", "IF6_polar", "IF8_polar", "IF9_polar")
## take out normal
# chr1 <- chr1_dd %>% select(pos,IF10_AF,IF9_AF,IF8_AF,IF6_AF)
## take out polarised
chr1 <- chr1_dd %>% dplyr::select(pos,IF10_polar,IF9_polar,IF8_polar,IF6_polar)
#################################
# Within each pool, create the segments
max_pos<-max(chr1$pos)+10
long_AFs<-data.frame(rbindlist(lapply(2:5,function(x){
# Get the pool
tmp<-data.frame(chr1[,c(1,x)])
# Bin the 0s
tmp<-tmp[tmp[,2] >= 0,]
# Set up xend
tmp$xend<-c(tmp$pos[2:nrow(tmp)],max_pos)
# Set up y/yend
tmp$y<-x-1.5
tmp$yend<-x-0.5
# Name pool
tmp$pool<-colnames(chr1)[x]
# Tidy
colnames(tmp)[2]<-"AFs"
return(tmp)
})))
## convert AFs to factor for plotting
long_AFs$chr1<-as.factor(long_AFs$AFs)
# rename for ease
chr1_long_AFs<- long_AFs
# Plot
LG1_geno <- ggplot(chr1_long_AFs,aes(x=pos,y=y))+
geom_segment(aes(xend=xend,yend=yend,colour=AFs))+
## CP detection
# geom_segment(data = CP,aes(x =x, y = y, xend = xend, yend = yend), colour="black", size = 1)+
viridis::scale_color_viridis(name = 'AF', option="magma")+
# ggtitle("IF9 polarised AFs")+
theme_classic()+
theme(axis.text.x=element_text(family = "Avenir", size=18),
axis.ticks.x=element_line(),
axis.ticks.y = element_blank(),
axis.text.y=element_text(family = "Avenir", size=20, angle=90, hjust=0.5,
colour=c("#3CBB75", "#481567", "#2D708E", "#B22222")),
axis.title.x=element_text(family="Avenir", size=30, vjust =-2),
axis.title.y=element_text(size=30, family="Avenir"),
legend.title = element_blank(),
# legend.key.size = unit(2,"line"),
# legend.text = element_text("Avenir", size=20),
legend.position = "none")+
scale_x_continuous(name="LG1 (Mb)",
breaks=seq(0,34000000, by = 1000000),
labels=seq(0,34, by = 1))+
scale_y_continuous(name = "AFs",
breaks = seq(1,4, by = 1),
labels=c("Iso\nY10", "Iso\nY9", "Iso\nY8", "Iso\nY6"))
ggsave(width = 30, height = 12, units = "cm", dpi=800, "~/Dropbox/Sussex_Guppies/Analyses/pool-seq/Figures/LG1_AF_plot_Isoy9-polarised.png", LG1_geno)
#########################################
## LG12 plot ##
#########################################
## read in LG12 data:
chr12 <- data.frame(fread("~/Dropbox/Sussex_Guppies/Analyses/pool-seq/poolfstat/outputs/final/chr12_AFs_final.tsv", header=TRUE))
## Polarise to IF9:
## remove pos
tmp <- chr12 %>% dplyr::select(IF10_AF, IF6_AF, IF8_AF, IF9_AF)
## save the IF9 freqs:
IF9_freqs<-tmp$IF9_AF
## polarise to Iso-Y9
for(i in colnames(tmp)){
tmp[IF9_freqs < 0.5,i]<-(1-tmp[IF9_freqs < 0.5,i])
}
## add IF9 polarised back in back in:
chr12_dd <- cbind(chr12,tmp)
colnames(chr12_dd) <- c("chr", "pos", "REF", "ALT", "IF10_AF", "IF6_AF", "IF8_AF", "IF9_AF",
"IF10_polar", "IF6_polar", "IF8_polar", "IF9_polar")
## take out polarised
chr12 <- chr12_dd %>% dplyr::select(pos,IF10_polar,IF9_polar,IF8_polar,IF6_polar)
#################################
# create segments
max_pos<-max(chr12$pos)+10
long_AFs<-data.frame(rbindlist(lapply(2:5,function(x){
# Get the pool
tmp<-data.frame(chr12[,c(1,x)])
# Bin the 0s
tmp<-tmp[tmp[,2] >= 0,]
# Set up xend
tmp$xend<-c(tmp$pos[2:nrow(tmp)],max_pos)
# Set up y/yend
tmp$y<-x-1.5
tmp$yend<-x-0.5
# Name pool
tmp$pool<-colnames(chr12)[x]
# Tidy
colnames(tmp)[2]<-"AFs"
return(tmp)
})))
## convert AFs to factor for plotting
long_AFs$chr12<-as.factor(long_AFs$AFs)
# rename for plotting
chr12_long_AFs <- long_AFs
## plot
LG12_geno <- ggplot(chr12_long_AFs,aes(x=pos,y=y))+
geom_segment(aes(xend=xend,yend=yend,colour=AFs))+
viridis::scale_color_viridis(name = 'AF', option="magma")+
theme_classic()+
theme(axis.text.x=element_text(family = "Avenir", size=18),
axis.ticks.x=element_line(),
axis.ticks.y = element_blank(),
axis.text.y=element_text(family = "Avenir", size=20, angle=90, hjust=0.5,
colour=c("#3CBB75", "#481567", "#2D708E", "#B22222")),
axis.title.x=element_text(family="Avenir", size=30, vjust =-2),
axis.title.y=element_text(size=30, family="Avenir"),
legend.title = element_blank(),
legend.position = "none")+
scale_x_continuous(name="LG12 (Mb)",
breaks=seq(0,34000000, by = 1000000),
labels=seq(0,34, by = 1))+
scale_y_continuous(name = "AFs",
breaks = seq(1,4, by = 1),
labels=c("Iso\nY10", "Iso\nY9", "Iso\nY8", "Iso\nY6"))
ggsave(width = 30, height = 12, units = "cm", dpi=800, "~/Dropbox/Sussex_Guppies/Analyses/pool-seq/Figures/LG12_AF_plot_Isoy9-polarised.png", LG1_geno)
## Can also look at folded AFs, e.g.:
chr12 <- data.frame(fread("~/Dropbox/Sussex_Guppies/Analyses/pool-seq/poolfstat/outputs/final/chr12_AFs_final.tsv", header=TRUE))
## fold AFs
chr12$IF10_folded = ifelse(chr12$IF10_AF < 0.5, abs(chr12$IF10_AF - 1), chr12$IF10_AF )
chr12$IF6_folded = ifelse(chr12$IF6_AF < 0.5, abs(chr12$IF6_AF - 1), chr12$IF6_AF )
chr12$IF8_folded = ifelse(chr12$IF8_AF < 0.5, abs(chr12$IF8_AF - 1), chr12$IF8_AF )
chr12$IF9_folded = ifelse(chr12$IF9_AF < 0.5, abs(chr12$IF9_AF - 1), chr12$IF9_AF )
## Polarise to IF9:
## remove pos
tmp <- chr12 %>% dplyr::select(IF10_AF, IF6_AF, IF8_AF, IF9_AF)
## save the IF9 freqs:
IF9_freqs<-tmp$IF9_AF
for(i in colnames(tmp)){
tmp[IF9_freqs < 0.5,i]<-(1-tmp[IF9_freqs < 0.5,i])
}
## add IF9 polarised back in back in:
chr12_dd <- cbind(chr12,tmp)
colnames(chr12_dd) <- c("chr", "pos", "REF", "ALT", "IF10_AF", "IF6_AF", "IF8_AF", "IF9_AF",
"IF10_folded", "IF6_folded", "IF8_folded", "IF9_folded",
"IF10_polar", "IF6_polar", "IF8_polar", "IF9_polar")
## take out folded
chr12 <- chr12_dd %>% dplyr::select(pos,IF10_folded,IF9_folded,IF8_folded,IF6_folded)
#################################
# create segments
max_pos<-max(chr12$pos)+10
long_AFs<-data.frame(rbindlist(lapply(2:5,function(x){
# Get the pool
tmp<-data.frame(chr12[,c(1,x)])
# Bin the 0s
tmp<-tmp[tmp[,2] >= 0,]
# Set up xend
tmp$xend<-c(tmp$pos[2:nrow(tmp)],max_pos)
# Set up y/yend
tmp$y<-x-1.5
tmp$yend<-x-0.5
# Name pool
tmp$pool<-colnames(chr12)[x]
# Tidy
colnames(tmp)[2]<-"AFs"
return(tmp)
})))
long_AFs$chr12<-as.factor(long_AFs$AFs)
chr12_long_AFs <- long_AFs
## plot
LG12_AFs_folded <- ggplot(chr12_long_AFs,aes(x=pos,y=y))+
geom_segment(aes(xend=xend,yend=yend,colour=AFs))+
viridis::scale_color_viridis(name = 'AF', option="magma")+
theme_classic()+
theme(axis.text.x=element_text(family = "Avenir", size=18),
axis.ticks.x=element_line(),
axis.ticks.y = element_blank(),
axis.text.y=element_text(family = "Avenir", size=20, angle=90, hjust=0.5,
colour=c("#3CBB75", "#481567", "#2D708E", "#B22222")),
axis.title.x=element_text(family="Avenir", size=30, vjust =-2),
axis.title.y=element_text(size=30, family="Avenir"),
legend.title = element_blank(),
legend.position = "none")+
scale_x_continuous(name="LG12 (Mb)",
breaks=seq(0,34000000, by = 1000000),
labels=seq(0,34, by = 1))+
scale_y_continuous(name = "AFs",
breaks = seq(1,4, by = 1),
labels=c("Iso\nY10", "Iso\nY9", "Iso\nY8", "Iso\nY6"))