Mercurial > repos > marie-tremblay-metatoul > normalization

comparison DrawSpec.R @ 5:3d00a98974b7 draft

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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
author lecorguille
date Tue, 02 Oct 2018 12:14:47 -0400
parents 966fcf7ae66e
children
comparison
equal deleted inserted replaced
4:8178d9a118e3 5:3d00a98974b7
1 drawSpec <- function (X, startP = -1, endP = -1, groupLabel = NULL, useLog = -1, highBound = -1, lowBound = -1,
2 xlab = NULL, ylab = NULL, main = NULL, nAxisPos = 4, offside = 0)
3 {
4 groupLabel_name = groupLabel
5 X = as.data.frame(X)
6 # colnames(X) = c(1:ncol(X))
7 X = as.matrix(X)
8 if (highBound != -1) {
9 for (i in 1:nrow(X)) {
10 myIndex = which(X[i, ] > highBound)
11 X[i, myIndex] = highBound
12 }
13 }
14 if (lowBound != -1) {
15 for (i in 1:nrow(X)) {
16 myIndex = which(X[i, ] < lowBound)
17 X[i, myIndex] = lowBound
18 }
19 }
20 if (is.null(groupLabel)) {
21 groupLabel = c(1:nrow(X))
22 groupLabel = as.factor(groupLabel)
23 }
24 else {
25 levels(groupLabel) = c(1:length(levels(groupLabel)))
26 }
27 if (startP == -1)
28 startP = 1
29 if (endP == -1)
30 endP = ncol(X)
31 if (is.null(xlab)) {
32 xlab = "index"
33 }
34 if (is.null(ylab)) {
35 ylab = "intensity"
36 }
37 if (is.null(main)) {
38 main = paste(" ", startP + offside, "-", endP + offside)
39 }
40 GraphRange <- c(startP:endP)
41 yn <- X[, GraphRange]
42 if (useLog != -1)
43 yn = log(yn)
44 if (length(yn) > ncol(X))
45 {
46 plot(yn[1, ], ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n")
47 tempVal = trunc(length(GraphRange)/nAxisPos)
48 xPos = c(0:nAxisPos) * tempVal
49 axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside])
50 for (i in 1:length(levels(groupLabel)))
51 {
52 groupLabelIdx = which(groupLabel == levels(groupLabel)[i])
53 color <- palette(rainbow(length(levels(groupLabel))))
54 for (j in 1:length(groupLabelIdx))
55 {
56 lines(yn[groupLabelIdx[j], ], col = color[i])
57 }
58 }
59 if (!is.null(groupLabel_name))
60 {
61 legendPos = "topleft"
62 legend(legendPos, levels(groupLabel_name), col = as.integer(levels(groupLabel)), text.col = "black", pch = c(19, 19), bg = "gray90")
63 }
64 }
65 if (length(yn) == ncol(X))
66 {
67 plot(yn, ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n")
68 tempVal = trunc(length(GraphRange)/nAxisPos)
69 xPos = c(0:nAxisPos) * tempVal
70 # axis(1, at = xPos, labels = xPos + startP + offside)
71 axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside])
72 lines(yn)
73 }
74 }