annotate plot_generic_x_y_plot.R @ 2:5aef8588b14e draft default tip

planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
author bebatut
date Mon, 18 Apr 2016 11:09:40 -0400
parents c0e2af569838
children
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c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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1 library('getopt')
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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2
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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3 option_specification = matrix(c(
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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4 'input_file', 'a', 2, 'character',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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5 'output_pdf_file', 'b', 2, 'character',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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6 'output_png_file', 'c', 2, 'character',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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7 'output_svg_file', 'd', 2, 'character',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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8 'x_column_id', 'e', 2, 'integer',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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9 'y_column_id', 'f', 2, 'integer',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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10 'xlog', 'g', 2, 'logical',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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11 'ylog', 'h', 2, 'logical',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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12 'xlab', 'i', 2, 'character',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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13 'ylab', 'j', 2, 'character',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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14 'col', 'k', 2, 'character',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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15 'pch', 'l', 2, 'integer',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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16 'lim', 'm', 2, 'logical',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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17 'abline', 'n', 2, 'logical',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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18 'bottom_margin', 'o', 2, 'integer',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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19 'left_margin', 'p', 2, 'integer',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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20 'top_margin', 'q', 2, 'integer',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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21 'right_margin', 'r', 2, 'integer',
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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22 'header','s',2,'logical'
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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23 ), byrow=TRUE, ncol=4);
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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24
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25 options = getopt(option_specification);
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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27 header = TRUE
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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28 if(!is.null(options$header)) header = options$header
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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30 data = read.table(options$input_file, sep = '\t', h = header)
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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32 x_column_id = 2
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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33 if(!is.null(options$x_column_id)) x_column_id = options$x_column_id
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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34 x_axis = data[,x_column_id]
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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35
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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36 y_column_id = 3
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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37 if(!is.null(options$y_column_id)) y_column_id = options$y_column_id
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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38 y_axis = data[,y_column_id]
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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39
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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40 xlim = c(min(x_axis),max(x_axis))
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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41 ylim = c(min(y_axis),max(y_axis))
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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42 if(!is.null(options$lim) && options$lim){
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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43 xlim = c(min(xlim,ylim), max(xlim,ylim))
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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44 ylim = xlim
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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45 }
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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46
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47
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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48 xlab = ""
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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49 if(!is.null(options$xlab)) xlab = options$xlab
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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50 ylab = ""
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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51 if(!is.null(options$ylab)) ylab = options$ylab
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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52
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53 col = 'grey25'
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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54 if(!is.null(options$col)) col = options$col
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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55
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56 pch = 21
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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57 if(!is.null(options$pch)) pch = options$pch
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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58
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59 log = ""
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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60 if(!is.null(options$xlog) && options$xlog) log = paste(log,"x",sep = '')
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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61 if(!is.null(options$ylog) && options$ylog) log = paste(log,"y",sep = '')
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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62
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63 margin = c(5,5,1,1)
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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64 if(!is.null(options$bottom_margin)) margin[1] = options$bottom_margin
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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65 if(!is.null(options$left_margin)) margin[2] = options$left_margin
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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66 if(!is.null(options$top_margin)) margin[3] = options$top_margin
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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67 if(!is.null(options$right_margin)) margin[4] = options$right_margin
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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68
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69 plot_generic_x_y_plot <- function(){
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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70 par(mar=margin)
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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71 plot(x_axis, y_axis, xlab = xlab, ylab = ylab,
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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72 col = col, log = log, xlim = xlim, ylim = ylim, pch = pch)
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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73 if(!is.null(options$abline) && options$abline) abline(a = 0, b = 1, col = 'grey50')
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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74 }
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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75
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76 if(!is.null(options$output_pdf_file)){
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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77 pdf(options$output_pdf_file)
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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78 plot_generic_x_y_plot()
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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79 dev.off()
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80 }
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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81
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82 if(!is.null(options$output_svg_file)){
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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83 svg(options$output_svg_file)
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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84 plot_generic_x_y_plot()
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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parents:
diff changeset
85 dev.off()
c0e2af569838 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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parents:
diff changeset
86 }