Mercurial > repos > artbio > small_rna_map

annotate small_rna_map.r @ 2:7feee0446c5c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
author artbio
date Wed, 12 Jul 2017 13:40:36 -0400
parents 2299eb1e7c93
children 2e0dc6032a98
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
1 library(optparse)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
2 library(ggplot2)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
3 library(gridExtra)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
4 library(RColorBrewer)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
5 library(gtable)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
6 library(grid)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
7
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
8 option_list <- list(
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
9 make_option(c("-r", "--output_tab"), type="character", help="path to tabular file"),
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
10 make_option("--output_pdf", type = "character", help="path to the pdf file with plot")
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
11 )
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
12
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
13 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
14 args = parse_args(parser)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
15
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
16 theme_set(theme_bw()) #a theme with a white background
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
17 Table = read.delim(args$output_tab, header=T, row.names=NULL)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
18 Table <- within(Table, Nbr_reads[Polarity=="R"] <- (Nbr_reads[Polarity=="R"]*-1))
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
19
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
20 #To assign colors to categorical variables in ggplot2 that have stable mapping
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
21 myColors <- brewer.pal(3,"Set1")
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
22 names(myColors) <- levels(Table$Polarity)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
23 colScale <- scale_colour_manual(name = "Polarity",values = myColors)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
24
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
25 #Make initial figures
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
26 p <- ggplot(Table, aes(x=Coordinate, y=Nbr_reads, colour=Polarity)) +
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
27 colScale+
2
7feee0446c5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
artbio
parents: 1
diff changeset
28 geom_segment(aes(y = 0, x = Coordinate, yend = Nbr_reads, xend = Coordinate, color=Polarity), alpha=1) +
7feee0446c5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
artbio
parents: 1
diff changeset
29 geom_segment(aes(y = Nbr_reads, x = 0, yend=Nbr_reads, xend=Chrom_length), alpha=0)+
0
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
30 facet_wrap(Dataset~Chromosome, scales="free", nrow=1, labeller = label_wrap_gen(multi_line = FALSE))+
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
31 scale_y_continuous(breaks = function(x) round(pretty(seq(-(max(x) + 1), (max(x) + 1)))))+#to display only integer values on y axis
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
32 geom_hline(yintercept=0, size=0.3)+
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
33 theme(strip.text = element_text(size = 6, lineheight = 0.1), #specify strip size
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
34 panel.grid.major = element_line(colour = "#ffffff"),#conceal major grid lines
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
35 panel.grid.minor = element_line(colour = "#ffffff"),#conceal minor grid lines
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
36 axis.title = element_blank(),# Conceal axis titles
1
2299eb1e7c93 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit d0362e589eb42377b7f10dfcec78be0288220755
artbio
parents: 0
diff changeset
37 axis.text = element_text(size = 6),#modify the size of tick labels along axes
2299eb1e7c93 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit d0362e589eb42377b7f10dfcec78be0288220755
artbio
parents: 0
diff changeset
38 legend.position = "none") # Hide the repeate caption
2299eb1e7c93 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit d0362e589eb42377b7f10dfcec78be0288220755
artbio
parents: 0
diff changeset
39
2299eb1e7c93 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit d0362e589eb42377b7f10dfcec78be0288220755
artbio
parents: 0
diff changeset
40 # Create legend
2299eb1e7c93 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit d0362e589eb42377b7f10dfcec78be0288220755
artbio
parents: 0
diff changeset
41 mylegend <- legendGrob(c("F", "R", "Median", "Mean"), pch=22,
2299eb1e7c93 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit d0362e589eb42377b7f10dfcec78be0288220755
artbio
parents: 0
diff changeset
42 gp=gpar(col = c("red","blue","black","yellow"), fill = c("red","blue","black","yellow")))
0
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
43
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
44 # The second plot
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
45 cols<- c("Median"="#000000", "Mean"="#fffa00")
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
46 p2 <- ggplot(Table, aes(x = Coordinate, group=1)) +
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
47 geom_point(aes(y=Median, colour="Median"), alpha=1, size = 1) +
2
7feee0446c5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
artbio
parents: 1
diff changeset
48 geom_point(aes(y=Mean, colour="Mean"), alpha= 0.5, size = 1.2)+
0
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
49 scale_colour_manual(name="", values=cols)+
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
50 expand_limits(y = seq(0,max(Table$Median),by=5)) +
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
51 facet_wrap(Dataset~Chromosome, scales="free", nrow=1, labeller = label_wrap_gen(multi_line = FALSE))+
2
7feee0446c5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
artbio
parents: 1
diff changeset
52 geom_segment(aes(y = Nbr_reads, x = 0, yend=Nbr_reads, xend=Chrom_length), alpha=0)+
7feee0446c5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
artbio
parents: 1
diff changeset
53 scale_y_continuous(limits = c(0,max(Table$Median)), position = "left")+
7feee0446c5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
artbio
parents: 1
diff changeset
54 theme(strip.background = element_blank(),
7feee0446c5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
artbio
parents: 1
diff changeset
55 strip.text.x = element_blank(),
0
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
56 panel.background = element_rect(fill = NA),
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
57 panel.grid.major = element_blank(),
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
58 panel.grid.minor = element_blank(),
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
59 panel.border = element_rect(fill = NA, colour = "grey50"),
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
60 axis.text = element_text(size = 6),
2
7feee0446c5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
artbio
parents: 1
diff changeset
61 axis.title = element_blank(),
7feee0446c5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
artbio
parents: 1
diff changeset
62 legend.position = "none")
1
2299eb1e7c93 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit d0362e589eb42377b7f10dfcec78be0288220755
artbio
parents: 0
diff changeset
63
0
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
64 # Transforme ggplot graphs on list of graphs
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
65 plot.list1 <- by(data = Table,
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
66 INDICES = c(Table$Chromosome),
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
67 simplify = TRUE,
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
68 FUN = function(x) {
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
69 p %+% x
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
70 })
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
71
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
72 plot.list2 <- by(data = Table,
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
73 INDICES = c(Table$Chromosome),
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
74 simplify = TRUE,
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
75 FUN = function(x) {
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
76 p2 %+% x
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
77 })
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
78
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
79 # Plotting in multiple pages with different rows
2
7feee0446c5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
artbio
parents: 1
diff changeset
80 multi.plot<-do.call(marrangeGrob,list(grobs=rbind(plot.list1,plot.list2),ncol=1,nrow=8,top=NULL,
7feee0446c5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
artbio
parents: 1
diff changeset
81 bottom="Coordinates(nt)", left="Number of reads / Median & Mean", right= mylegend))
0
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
82 ggsave(args$output_pdf, device="pdf", plot=multi.plot, height=11.69, width=8.2)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
parents:
diff changeset
83