Mercurial > repos > bebatut > plot_barplot

annotate plot_barplot.R @ 5:2a9b68111074 draft default tip

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 5653f2982dc5aeccd7701970fdfea444e3e53e3c-dirty
author bebatut
date Wed, 18 May 2016 12:25:52 -0400
parents f8cec112f5f9
children
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de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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diff changeset
1 library('getopt')
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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3 option_specification = matrix(c(
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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4 'input_file', 'i', 2, 'character',
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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5 'output_pdf_file', 'p', 2, 'character',
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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6 'output_png_file', 'o', 2, 'character',
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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7 'output_svg_file', 's', 2, 'character',
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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8 'data_column', 'd', 2, 'integer',
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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9 'names_column', 'n', 2, 'integer',
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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10 'xlab', 'x', 2, 'character',
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11 'log', 'g', 2, 'logical',
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de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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12 'col', 'c', 2, 'character',
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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13 'bottom_margin', 'b', 2, 'integer',
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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14 'left_margin', 'l', 2, 'integer',
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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15 'top_margin', 't', 2, 'integer',
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16 'right_margin', 'r', 2, 'integer',
f8cec112f5f9 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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17 'header','y',2,'logical'
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18 ), byrow=TRUE, ncol=4);
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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20 options = getopt(option_specification);
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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22 header = TRUE
f8cec112f5f9 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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23 if(!is.null(options$header)) header = options$header
f8cec112f5f9 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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f8cec112f5f9 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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25 data = read.table(options$input_file, sep = '\t', h = header)
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de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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27 data_column = 2
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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28 if(!is.null(options$data_column)) data_column = options$data_column
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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29 names_column = 1
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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30 if(!is.null(options$names_column)) names_column = options$names_column
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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32 margin = c(5,19,1,1)
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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33 if(!is.null(options$bottom_margin)) margin[1] = options$bottom_margin
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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34 if(!is.null(options$left_margin)) margin[2] = options$left_margin
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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35 if(!is.null(options$top_margin)) margin[3] = options$top_margin
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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36 if(!is.null(options$right_margin)) margin[4] = options$right_margin
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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38 xlab = ""
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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39 if(!is.null(options$xlab)) xlab = options$xlab
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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41 col = "grey"
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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42 if(!is.null(options$col)) col = options$col
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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44 log = ""
2a9b68111074 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 5653f2982dc5aeccd7701970fdfea444e3e53e3c-dirty
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45 if(!is.null(options$log) && options$log) log = "x"
2a9b68111074 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 5653f2982dc5aeccd7701970fdfea444e3e53e3c-dirty
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46
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de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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47 plot_barplot <- function(){
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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48 par(las=2)
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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49 par(mar=margin)
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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50 barplot(data[, data_column], horiz = T, xlab = xlab,
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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51 names.arg = data[, names_column], col = col, cex.names=0.7,
5
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52 cex.axis = 0.8, log = log)
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53 }
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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55 if(!is.null(options$output_pdf_file)){
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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56 pdf(options$output_pdf_file)
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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57 plot_barplot()
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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58 dev.off()
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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59 }
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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61 if(!is.null(options$output_svg_file)){
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62 svg(options$output_svg_file)
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63 plot_barplot()
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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64 dev.off()
de039abf9641 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
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65 }