Mercurial > repos > artbio > small_rna_map

annotate small_rna_map.r @ 4:6ff925458e05 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit dcd643f146afe371d3e418aa91ddbaff6211a09a
author artbio
date Tue, 18 Jul 2017 17:35:52 -0400
parents 2e0dc6032a98
children d65045e976e6
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1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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1 library(optparse)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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2 library(ggplot2)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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3 library(gridExtra)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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4 library(RColorBrewer)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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5 library(gtable)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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6 library(grid)
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8 option_list <- list(
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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9 make_option(c("-r", "--output_tab"), type="character", help="path to tabular file"),
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10 make_option("--output_pdf", type = "character", help="path to the pdf file with plot")
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11 )
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1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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13 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
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14 args = parse_args(parser)
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1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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16 theme_set(theme_bw()) #a theme with a white background
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17 Table = read.delim(args$output_tab, header=T, row.names=NULL)
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18 Table <- within(Table, Nbr_reads[Polarity=="R"] <- (Nbr_reads[Polarity=="R"]*-1))
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19 Chr_limits <- unique(data.frame(Dataset=Table$Dataset, Chromosome=Table$Chromosome,
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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20 Chrom_length=Table$Chrom_length))
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21 Chr_limits_inf <- data.frame(Coordinate=Chr_limits$Chrom_length*0,
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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22 Nbr_reads=Chr_limits$Chrom_length*0,
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23 Polarity=rep("F", length(Chr_limits$Dataset)),
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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24 Max=Chr_limits$Chrom_length*0,
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25 Mean=Chr_limits$Chrom_length*0,
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26 Median=Chr_limits$Chrom_length*0)
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27 Chr_limits_inf <- cbind(Chr_limits, Chr_limits_inf)
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28 Chr_limits_sup <- data.frame(Coordinate=Chr_limits$Chrom_length+1,
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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29 Nbr_reads=Chr_limits$Chrom_length*0,
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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30 Polarity=rep("F", length(Chr_limits$Dataset)),
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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31 Max=Chr_limits$Chrom_length*0,
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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32 Mean=Chr_limits$Chrom_length*0,
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33 Median=Chr_limits$Chrom_length*0)
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34 Chr_limits_sup <- cbind(Chr_limits, Chr_limits_sup)
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35 Table <- rbind(Table, Chr_limits_inf, Chr_limits_sup)
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37 #To assign colors to categorical variables in ggplot2 that have stable mapping
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38 myColors <- brewer.pal(3,"Set1")
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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39 names(myColors) <- levels(Table$Polarity)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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40 colScale <- scale_colour_manual(name = "Polarity",values = myColors)
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42 #Make initial figures
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44 p <- ggplot(Table, aes(x=Coordinate, y=Nbr_reads, colour=Polarity)) +
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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45 colScale+
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46 geom_segment(aes(y = 0, x = Coordinate, yend = Nbr_reads, xend = Coordinate, color=Polarity)) +
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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47 # geom_segment(aes(y = Nbr_reads, x = 0, yend=Nbr_reads, xend=Chrom_length), alpha=0)+
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1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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48 facet_wrap(Dataset~Chromosome, scales="free", nrow=1, labeller = label_wrap_gen(multi_line = FALSE))+
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49 # scale_x_continuous(limits = c(rep(0, length(Table$Chromosome)), Chr_lengths$Chrom_length)) +
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50 scale_y_continuous(breaks = function(x) round(pretty(seq(-(max(x) + 1), (max(x) + 1)))))+ # to display only integer values on y axis
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51 geom_hline(yintercept=0, size=0.3)+
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52 theme(strip.text = element_text(size = 6, lineheight = 0.1), #specify strip size
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53 panel.grid.major = element_line(colour = "#ffffff"),#conceal major grid lines
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54 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
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55 axis.title = element_blank(),# Conceal axis titles
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56 axis.text = element_text(size = 6),#modify the size of tick labels along axes
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57 legend.position = "none") # Hide the repeate caption
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58
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59 # Create legend
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60 mylegend <- legendGrob(c("F", "R", "Median", "Mean"), pch=22,
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61 gp=gpar(col = c("red","blue","black","yellow"), fill = c("red","blue","black","yellow")))
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63 # The second plot
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64 cols<- c("Median"="#000000", "Mean"="#fffa00")
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65 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
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66 geom_point(aes(y=Median, colour="Median"), alpha=1, size = 1) +
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67 geom_point(aes(y=Mean, colour="Mean"), alpha= 0.5, size = 1.2)+
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68 scale_colour_manual(name="", values=cols)+
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69 expand_limits(y = seq(0,max(Table$Median),by=5)) +
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70 facet_wrap(Dataset~Chromosome, scales="free", nrow=1, labeller = label_wrap_gen(multi_line = FALSE))+
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71 # geom_segment(aes(y = Nbr_reads, x = 0, yend=Nbr_reads, xend=Chrom_length), alpha=0)+
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72 scale_y_continuous(limits = c(0,max(Table$Median)), position = "left")+
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73 theme(strip.background = element_blank(),
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74 strip.text.x = element_blank(),
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75 panel.background = element_rect(fill = NA),
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76 panel.grid.major = element_blank(),
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77 panel.grid.minor = element_blank(),
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78 panel.border = element_rect(fill = NA, colour = "grey50"),
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79 axis.text = element_text(size = 6),
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80 axis.title = element_blank(),
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81 legend.position = "none")
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83 # Transforme ggplot graphs on list of graphs
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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84 plot.list1 <- by(data = Table,
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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85 INDICES = c(Table$Chromosome),
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2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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86 #simplify = TRUE,
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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87 FUN = function(x) {p %+% x }
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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88 )
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1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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89
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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90 plot.list2 <- by(data = Table,
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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91 INDICES = c(Table$Chromosome),
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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92 simplify = TRUE,
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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93 FUN = function(x) {
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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94 p2 %+% x
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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95 })
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2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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96
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1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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97 # Plotting in multiple pages with different rows
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2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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98
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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99 grobs=rbind(plot.list1,plot.list2)
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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100 multi.plot<-do.call(marrangeGrob,list(grobs,ncol=1,nrow=8,top=NULL,
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7feee0446c5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
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101 bottom="Coordinates(nt)", left="Number of reads / Median & Mean", right= mylegend))
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2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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102 ggsave(args$output_pdf, device="pdf", plot=multi.plot, height=11.69, width=8.2)