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1 #!/usr/bin/R
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2
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3 # R script to call Vennerable package from galaxy
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4 # info: alex.bossers@wur.nl
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5 #
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6 # version:
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7 # 2015-04-21 fixed <NA> values bug
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8 # .......... Initial version
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9 #
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10
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11 # R --slave --vanilla --file=PlotBar.R --args inputFile x_data weighting outputFile plottype resolution imagetype
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12 # 1 2 3 4 5 6 7 8 9 10 11 12
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13
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14 #get cmd line args
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15 args <- commandArgs()
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16 in.file <- args[6]
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17 xData <- args[7] # data labels xData of format "a, b, c" and can include spaces
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18 weighting <- args[8]
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19 out.file <- args[9]
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20 plottype <- args[10]
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21 resolution <- args[11] # in dpi
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22 imagetype <- args[12] # svg, pdf or png
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23
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24 #open lib
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25 library(Vennerable)
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26 options(bitmapType='cairo')
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27
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28 # for labels of bars or bar groups presume column names from data
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29 if (xData != "default") {
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30 # read without header input file (must be tabular)
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31 a_data <- read.delim(in.file, header=F, na.strings="") # replace empty by <NA> for TAB delimited file
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32 colnames (a_data) <- strsplit(xData,",")[[1]] # insert headers from galaxy input
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33 annot_data <- lapply(a_data, na.omit) # remove empty values for counting
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34 Vannot <- Venn(annot_data)
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35 } else {
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36 # read with header input file (must be tabular)
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37 a_data <- read.delim(in.file, na.strings="") # replace any empty values by <NA> for AB delimited headered file
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38 annot_data <- lapply(a_data, na.omit) # remove empty values for counting
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39 Vannot <- Venn(annot_data)
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40 }
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41
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42 #set output imagetype (svg pdf or png)
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43 #R 3.0.2 and default cairo libs should handle it all ok
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44 #it could be that X11 should be loaded for non-pdf
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45 if (imagetype == "svg") {
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46 svg(out.file)
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47 } else if (imagetype == "png") {
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48 png(out.file, width = 1600, height = 1600, res = resolution)
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49 } else {
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50 pdf(out.file)
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51 }
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52
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53 # plot it
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54 if (plottype == "ChowRuskey") {
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55 plot(Vannot, type = plottype)
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56
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57 } else if (plottype == "AWFE") {
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58 plot(Vannot, doWeights = weighting, type = plottype)
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59
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60 } else if (plottype == "circles") {
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61 plot(Vannot)
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62
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63 } else if (plottype == "ellipses"){
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64 plot(Vannot, type = "ellipses")
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65
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66 } else if (plottype == "squares"){
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67 plot(Vannot, type = "squares")
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68
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69 } else if (plottype == "battle"){
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70 plot(Vannot, type = "battle")
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71 }
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72
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73 cat ("Wrapper version 1.2c (empty value bug fixed), running Vennerable v3.0-82\n Info/bugs: alex.bossers@wur.nl\n")
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74 dev.off() |
