Mercurial > repos > petr-novak > repeatrxplorer

comparison lib/tarean/logo_methods.R @ 0:1d1b9e1b2e2f draft

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author petr-novak
date Thu, 19 Dec 2019 10:24:45 -0500
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-1:000000000000 0:1d1b9e1b2e2f
1 #! /usr/bin/env Rscript
2
3 ## FUNCTIONS:
4 letterA <- function(x.pos,y.pos,ht,wt,id=NULL){
5
6 x <- c(0,4,6,10,8,6.8,3.2,2,0,3.6,5,6.4,3.6)
7 y <- c(0,10,10,0,0,3,3,0,0,4,7.5,4,4)
8 x <- 0.1*x
9 y <- 0.1*y
10
11 x <- x.pos + wt*x
12 y <- y.pos + ht*y
13
14 if (is.null(id)){
15 id <- c(rep(1,9),rep(2,4))
16 }else{
17 id <- c(rep(id,9),rep(id+1,4))
18 }
19
20 fill <- c("green","white")
21
22 list(x=x,y=y,id=id,fill=fill)
23 }
24
25 ## T
26 letterT <- function(x.pos,y.pos,ht,wt,id=NULL){
27
28 x <- c(0,10,10,6,6,4,4,0)
29 y <- c(10,10,9,9,0,0,9,9)
30 x <- 0.1*x
31 y <- 0.1*y
32
33 x <- x.pos + wt*x
34 y <- y.pos + ht*y
35
36 if (is.null(id)){
37 id <- rep(1,8)
38 }else{
39 id <- rep(id,8)
40 }
41
42 fill <- "red"
43
44 list(x=x,y=y,id=id,fill=fill)
45 }
46
47 ## C
48 letterC <- function(x.pos,y.pos,ht,wt,id=NULL){
49 angle1 <- seq(0.3+pi/2,pi,length=100)
50 angle2 <- seq(pi,1.5*pi,length=100)
51 x.l1 <- 0.5 + 0.5*sin(angle1)
52 y.l1 <- 0.5 + 0.5*cos(angle1)
53 x.l2 <- 0.5 + 0.5*sin(angle2)
54 y.l2 <- 0.5 + 0.5*cos(angle2)
55
56 x.l <- c(x.l1,x.l2)
57 y.l <- c(y.l1,y.l2)
58
59 x <- c(x.l,rev(x.l))
60 y <- c(y.l,1-rev(y.l))
61
62 x.i1 <- 0.5 +0.35*sin(angle1)
63 y.i1 <- 0.5 +0.35*cos(angle1)
64 x.i1 <- x.i1[y.i1<=max(y.l1)]
65 y.i1 <- y.i1[y.i1<=max(y.l1)]
66 y.i1[1] <- max(y.l1)
67
68 x.i2 <- 0.5 +0.35*sin(angle2)
69 y.i2 <- 0.5 +0.35*cos(angle2)
70
71 x.i <- c(x.i1,x.i2)
72 y.i <- c(y.i1,y.i2)
73
74 x1 <- c(x.i,rev(x.i))
75 y1 <- c(y.i,1-rev(y.i))
76
77 x <- c(x,rev(x1))
78 y <- c(y,rev(y1))
79
80 x <- x.pos + wt*x
81 y <- y.pos + ht*y
82
83 if (is.null(id)){
84 id <- rep(1,length(x))
85 }else{
86 id <- rep(id,length(x))
87 }
88
89 fill <- "blue"
90
91 list(x=x,y=y,id=id,fill=fill)
92 }
93
94
95 ## G
96 letterG <- function(x.pos,y.pos,ht,wt,id=NULL){
97 angle1 <- seq(0.3+pi/2,pi,length=100)
98 angle2 <- seq(pi,1.5*pi,length=100)
99 x.l1 <- 0.5 + 0.5*sin(angle1)
100 y.l1 <- 0.5 + 0.5*cos(angle1)
101 x.l2 <- 0.5 + 0.5*sin(angle2)
102 y.l2 <- 0.5 + 0.5*cos(angle2)
103
104 x.l <- c(x.l1,x.l2)
105 y.l <- c(y.l1,y.l2)
106
107 x <- c(x.l,rev(x.l))
108 y <- c(y.l,1-rev(y.l))
109
110 x.i1 <- 0.5 +0.35*sin(angle1)
111 y.i1 <- 0.5 +0.35*cos(angle1)
112 x.i1 <- x.i1[y.i1<=max(y.l1)]
113 y.i1 <- y.i1[y.i1<=max(y.l1)]
114 y.i1[1] <- max(y.l1)
115
116 x.i2 <- 0.5 +0.35*sin(angle2)
117 y.i2 <- 0.5 +0.35*cos(angle2)
118
119 x.i <- c(x.i1,x.i2)
120 y.i <- c(y.i1,y.i2)
121
122 x1 <- c(x.i,rev(x.i))
123 y1 <- c(y.i,1-rev(y.i))
124
125 x <- c(x,rev(x1))
126 y <- c(y,rev(y1))
127
128 h1 <- max(y.l1)
129 r1 <- max(x.l1)
130
131 h1 <- 0.4
132 x.add <- c(r1,0.5,0.5,r1-0.2,r1-0.2,r1,r1)
133 y.add <- c(h1,h1,h1-0.1,h1-0.1,0,0,h1)
134
135
136
137 if (is.null(id)){
138 id <- c(rep(1,length(x)),rep(2,length(x.add)))
139 }else{
140 id <- c(rep(id,length(x)),rep(id+1,length(x.add)))
141 }
142
143 x <- c(rev(x),x.add)
144 y <- c(rev(y),y.add)
145
146 x <- x.pos + wt*x
147 y <- y.pos + ht*y
148
149
150 fill <- c("orange","orange")
151
152 list(x=x,y=y,id=id,fill=fill)
153
154 }
155
156 Letter <- function(which,x.pos,y.pos,ht,wt){
157
158 if (which == "A"){
159 letter <- letterA(x.pos,y.pos,ht,wt)
160 }else if (which == "C"){
161 letter <- letterC(x.pos,y.pos,ht,wt)
162 }else if (which == "G"){
163 letter <- letterG(x.pos,y.pos,ht,wt)
164 }else if (which == "T"){
165 letter <- letterT(x.pos,y.pos,ht,wt)
166 }else{
167 stop("which must be one of A,C,G,T")
168 }
169
170 letter
171 }
172
173
174
175
176 plot_multiline_logo = function(cons.logo,read=NULL, W=50, setpar=TRUE, gaps = NULL){
177 ## logo - base order - A C G T
178 if (ncol(cons.logo)==5){
179 gaps_prob = cons.logo[,5]
180 }else{
181 gaps_prob = NULL
182 }
183 ps=10 # Point_Size
184 tm=4
185 pwm=as.matrix(cons.logo[,1:4])
186 N=nrow(pwm)
187 Nori=N
188 if (N<W){
189 W=N
190 }
191 s1=seq(1,N,by=W)
192 s2=seq(W,N,by=W)
193 if (length(s2)<length(s1)){
194 pwm=rbind(pwm,matrix(0,nrow=W*length(s1)-N,ncol=4,dimnames=list(NULL,c('A','C','G','T'))))
195 if (!is.null(read)){
196 pwm_read = rbind(read,matrix(0,nrow=W*length(s1)-N,ncol=4,dimnames=list(NULL,c('A','C','G','T'))))
197 }
198 N=nrow(pwm)
199 s2=seq(W,N,by=W)
200 }
201 if (setpar){
202 par(mfrow = c(ceiling(N/W),1), mar=c(1,4,1,0))
203 }
204 for (i in seq_along(s1)){
205 if (!is.null(read)){
206 plot.logo(pwm_read[s1[i]:s2[i],],maxh=2)
207 }
208 plot.logo(pwm[s1[i]:s2[i],],maxh=max(rowSums(cons.logo)))
209 if(!is.null(gaps)){
210 ## transparent rectangles
211 rect((gaps[ ,'start']-s1[i]+1),0, (gaps[,'end']-s1[i]+2), max(pwm), col="#00000005")
212
213 }
214 if(!is.null(gaps_prob)){
215 rect(seq_along(s1[i]:s2[i]),
216 max(rowSums(cons.logo)),
217 seq_along(s1[i]:s2[i])+1,
218 max(rowSums(cons.logo)) - gaps_prob[s1[i]:s2[i]],
219 col="#00000030")
220
221
222 }
223 ticks=intersect(intersect(pretty(pretty(s1[i]:s2[i])+1),s1[i]:s2[i]),1:Nori)
224 axis(1,at=ticks+1.5-s1[i],label=ticks,tick=FALSE)
225 y=pretty(c(0,max(pwm)),n=tm)
226 axis(2,at=y,label=y,las=2,cex.axis=.7)
227 }
228 }
229
230 plot.logo=function(pwm,maxh=NULL){
231 acgt=c("A","C","G","T")
232 pwm = pwm[,acgt]
233 nbp=dim(pwm)[1]
234 if (is.null(maxh)) {maxh=max(rowSums(pwm))}
235
236 plot(0,0,xlim=c(0,nbp),ylim=c(0,maxh),type="n",axes=F,xlab="",ylab="")
237 for ( i in 1:nbp){
238 S=order(pwm[i,])
239 hgts=pwm[i,S]
240 nts=acgt[S]
241 ypos=c(0,cumsum(hgts)[1:3])
242 for (j in 1:4){
243 if (hgts[j]==0) next
244 L=Letter(which=nts[j],x.pos=i,y.pos=ypos[j],ht=hgts[j],wt=1)
245 Id=L$id==1
246 polygon(L$x[Id],L$y[Id],lty=0,col=L$fill[1])
247 if (sum(L$id==2)>0) {
248 polygon(L$x[!Id],L$y[!Id],lty=0,col=L$fill[2])
249 }
250 }
251 }
252 }
253
254
255