Mercurial > repos > marie-tremblay-metatoul > nmr_bucketing

annotate DrawSpec.R @ 9:62c62e31fc80 draft

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
author lecorguille
date Fri, 21 Apr 2017 08:53:40 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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9
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
1 drawSpec <- function (X, startP = -1, endP = -1, groupLabel = NULL, useLog = -1, highBound = -1, lowBound = -1,
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
2 xlab = NULL, ylab = NULL, main = NULL, nAxisPos = 4, offside = 0)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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3 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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diff changeset
4 groupLabel_name = groupLabel
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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5 X = as.data.frame(X)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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6 # colnames(X) = c(1:ncol(X))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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7 X = as.matrix(X)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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diff changeset
8 if (highBound != -1) {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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diff changeset
9 for (i in 1:nrow(X)) {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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10 myIndex = which(X[i, ] > highBound)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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11 X[i, myIndex] = highBound
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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12 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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13 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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diff changeset
14 if (lowBound != -1) {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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15 for (i in 1:nrow(X)) {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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16 myIndex = which(X[i, ] < lowBound)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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17 X[i, myIndex] = lowBound
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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18 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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19 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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20 if (is.null(groupLabel)) {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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diff changeset
21 groupLabel = c(1:nrow(X))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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22 groupLabel = as.factor(groupLabel)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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23 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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24 else {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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25 levels(groupLabel) = c(1:length(levels(groupLabel)))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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26 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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27 if (startP == -1)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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28 startP = 1
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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29 if (endP == -1)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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30 endP = ncol(X)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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31 if (is.null(xlab)) {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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32 xlab = "index"
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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33 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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34 if (is.null(ylab)) {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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35 ylab = "intensity"
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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36 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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37 if (is.null(main)) {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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38 main = paste(" ", startP + offside, "-", endP + offside)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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39 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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40 GraphRange <- c(startP:endP)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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41 yn <- X[, GraphRange]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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42 if (useLog != -1)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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43 yn = log(yn)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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44 if (length(yn) > ncol(X))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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45 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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46 plot(yn[1, ], ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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47 tempVal = trunc(length(GraphRange)/nAxisPos)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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48 xPos = c(0:nAxisPos) * tempVal
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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49 axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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diff changeset
50 for (i in 1:length(levels(groupLabel)))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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51 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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52 groupLabelIdx = which(groupLabel == levels(groupLabel)[i])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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53 color <- palette(rainbow(length(levels(groupLabel))))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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54 for (j in 1:length(groupLabelIdx))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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55 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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56 lines(yn[groupLabelIdx[j], ], col = color[i])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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57 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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58 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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59 if (!is.null(groupLabel_name))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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60 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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61 legendPos = "topleft"
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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62 legend(legendPos, levels(groupLabel_name), col = as.integer(levels(groupLabel)), text.col = "black", pch = c(19, 19), bg = "gray90")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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63 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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64 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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65 if (length(yn) == ncol(X))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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66 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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diff changeset
67 plot(yn, ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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68 tempVal = trunc(length(GraphRange)/nAxisPos)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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69 xPos = c(0:nAxisPos) * tempVal
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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70 # axis(1, at = xPos, labels = xPos + startP + offside)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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71 axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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72 lines(yn)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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73 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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74 }