Mercurial > repos > marie-tremblay-metatoul > nmr_preprocessing
annotate DrawFunctions.R @ 7:122df1bf0a8c draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
author | workflow4metabolomics |
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date | Fri, 11 Jul 2025 08:33:38 +0000 |
parents | 5e64657b4fe5 |
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rev | line source |
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7
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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1 library(ggplot2) # nice plots |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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2 library(gridExtra) # nice plots |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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3 library(reshape2) # data manipulation |
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5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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4 |
7
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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5 Draw <- function(Signal_data, type.draw = c("signal", "pca"), output = c( |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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6 "default", |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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7 "window", "png", "pdf" |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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8 ), dirpath = ".", filename = "%003d", height = 480, |
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5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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9 width = 640, pdf.onefile = TRUE, ...) { |
7
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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10 # Data initialisation and checks ---------------------------------------------- |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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11 type.draw <- match.arg(type.draw) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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12 output <- match.arg(output) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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13 fullpath <- paste(file.path(dirpath, filename), output, sep = ".") |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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14 createFile <- TRUE |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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15 createWindow <- FALSE |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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16 |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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17 # Drawing -------------------------------------------------------------------- |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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18 # output |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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19 switch(output, |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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20 default = { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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21 createFile <- FALSE |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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22 }, |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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23 window = { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
parents:
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24 createWindow <- TRUE |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
parents:
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25 createFile <- FALSE |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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26 }, |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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27 png = { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
parents:
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28 grDevices::png(fullpath, width, height) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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29 }, |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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30 pdf = { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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31 grDevices::pdf(fullpath, |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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32 width = width / 72, height = height / 72, |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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33 onefile = pdf.onefile |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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34 ) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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35 }, |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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36 { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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37 stop("Unknown output type.") |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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38 } |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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39 ) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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40 |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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41 # Drawing type (signal/spectrum or PCA) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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42 funs <- list(signal = DrawSignal, pca = DrawPCA) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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43 if (type.draw %in% names(funs)) { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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44 fun <- funs[[type.draw]] |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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45 } else { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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46 stop(paste("Unknown type:", type.draw)) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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47 } |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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48 |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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49 # Plot finalisation ---------------------------------------------- |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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50 if (is.vector(Signal_data)) { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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51 Signal_data <- vec2mat(Signal_data) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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52 } |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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53 fun(Signal_data, createWindow = createWindow, ...) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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54 if (createFile) { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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55 grDevices::dev.off() |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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56 } |
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5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
lecorguille
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57 } |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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58 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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59 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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60 |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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61 ##### DrawSignal |
5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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62 |
7
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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63 DrawSignal <- function(Signal_data, subtype = c( |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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64 "stacked", "together", |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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65 "separate", "diffmean", "diffmedian", "diffwith" |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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66 ), |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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67 ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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68 xlab = "rowname", RowNames = NULL, row = 1, num.stacked = 4, |
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5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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69 main = NULL, createWindow) { |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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70 # nticks |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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71 |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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72 # Data initialisation and checks ---------------------------------------------- |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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73 |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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74 subtype <- match.arg(subtype) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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75 vec <- is.vector(Signal_data) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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76 if (vec) { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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77 Signal_data <- vec2mat(Signal_data) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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78 } |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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79 |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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80 n <- nrow(Signal_data) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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81 m <- ncol(Signal_data) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
workflow4metabolomics
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82 |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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83 if (n < num.stacked) { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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84 num.stacked <- n |
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5e64657b4fe5
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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85 } |
7
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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86 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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87 scale <- colnames(Signal_data) |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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88 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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89 num.plot <- sum(ReImModArg) |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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90 |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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91 Var <- rowname <- value <- NULL # only for R CMD check |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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92 |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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93 # Drawing array |
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94 if (num.plot <= 0) { |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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95 stop("Nothing selected in ReImModArg.") |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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96 } else if (num.plot <= 2) { |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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97 if (vertical) { |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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98 nrow <- num.plot |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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99 ncol <- 1 |
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100 } else { |
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101 nrow <- 1 |
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102 ncol <- num.plot |
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103 } |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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104 } else { |
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105 nrow <- 2 |
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106 ncol <- 2 |
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107 } |
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108 |
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109 # RowNames |
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110 if (is.null(RowNames)) { |
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111 RowNames <- rownames(Signal_data) |
122df1bf0a8c
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112 if (is.null(RowNames)) { |
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113 RowNames <- 1:n |
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114 } |
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115 } else { |
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116 if (!is.vector(RowNames)) { |
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117 stop("RowNames is not a vector") |
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118 } |
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119 if (length(RowNames) != n) { |
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120 stop(paste("RowNames has length", length(RowNames), "and there are", n, "FIDs.")) |
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121 } |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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122 } |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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123 |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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124 if (n == 1) { |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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125 RowNames <- deparse(substitute(Signal_data)) |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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126 } |
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127 |
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128 elements <- list() |
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129 if (ReImModArg[1]) { |
122df1bf0a8c
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130 elements[["Re"]] <- Re(Signal_data) |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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131 rownames(elements[["Re"]]) <- RowNames |
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132 } |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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133 if (ReImModArg[2]) { |
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134 elements[["Im"]] <- Im(Signal_data) |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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135 rownames(elements[["Im"]]) <- RowNames |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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136 } |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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137 if (ReImModArg[3]) { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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138 elements[["Mod"]] <- Mod(Signal_data) |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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139 rownames(elements[["Mod"]]) <- RowNames |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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140 } |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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141 if (ReImModArg[4]) { |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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142 elements[["Arg"]] <- Arg(Signal_data) |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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143 rownames(elements[["Arg"]]) <- RowNames |
2
5e64657b4fe5
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lecorguille
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144 } |
7
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145 |
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146 |
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147 |
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148 |
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149 # Drawing -------------------------------------------------------------------- |
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150 |
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151 y <- x <- NULL # only for R CMD check |
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152 |
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153 |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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154 # SEPARATE or STACKED =============== |
122df1bf0a8c
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155 if (subtype == "separate" | subtype == "stacked") { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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156 i <- 1 |
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157 while (i <= n) { |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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158 if (createWindow) { |
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159 grDevices::dev.new(noRStudioGD = TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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160 } |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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161 if (subtype == "separate") { |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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162 # The other uses gridExtra to do that |
122df1bf0a8c
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163 graphics::par(mfrow = c(nrow, ncol)) |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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164 } |
122df1bf0a8c
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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165 plots <- list() |
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166 if (subtype == "separate") { |
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167 last <- i |
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168 } else { |
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169 last <- min(i + num.stacked - 1, n) |
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170 } |
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171 for (name in names(elements)) { |
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172 if (subtype == "separate") { |
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173 if (n == 1) { |
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174 df <- data.frame(x = as.numeric(scale), y = elements[[name]]) |
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175 } else { |
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176 df <- data.frame(x = as.numeric(scale), y = elements[[name]][i, ]) |
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177 } |
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178 |
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179 plots[[name]] <- ggplot2::ggplot(data = df, ggplot2::aes(x = x, y = y)) + |
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180 ggplot2::geom_line(size = 1) + |
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181 ggplot2::theme(legend.position = "none") + |
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182 ggplot2::labs(x = xlab, y = name) + |
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183 ggplot2::ggtitle(RowNames[i]) + |
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184 ggplot2::theme_bw() |
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185 |
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186 if ((df[1, "x"] - df[(dim(df)[1]), "x"]) > 0) { |
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187 plots[[name]] <- plots[[name]] + ggplot2::scale_x_reverse() |
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188 } |
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189 } else { |
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190 if (n == 1) { |
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191 melted <- data.frame( |
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192 rowname = rep(name, m), |
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193 Var = as.numeric(scale), value = elements[[name]][i, ] |
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194 ) |
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195 } else if (last == i) { |
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196 melted <- data.frame( |
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197 rowname = rep(rownames(elements[[name]])[i], m), |
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198 Var = as.numeric(scale), value = elements[[name]][i, ] |
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199 ) |
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200 } else { |
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201 melted <- reshape2::melt(elements[[name]][i:last, ], varnames = c("rowname", "Var")) |
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202 } |
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203 |
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204 |
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205 plots[[name]] <- ggplot2::ggplot(data = melted, ggplot2::aes(x = Var, y = value)) + |
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206 ggplot2::geom_line(size = 0.3) + |
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207 ggplot2::facet_grid(rowname ~ ., scales = "free_y") + |
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208 ggplot2::theme(legend.position = "none") + |
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209 ggplot2::labs(x = xlab, y = name) + |
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210 ggplot2::ggtitle(label = main) + |
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211 ggplot2::theme_bw() |
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212 |
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213 if ((melted[1, "Var"] - melted[(dim(melted)[1]), "Var"]) > 0) { |
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214 plots[[name]] <- plots[[name]] + ggplot2::scale_x_reverse() |
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215 } |
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216 } |
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217 } |
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218 |
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219 if (subtype == "stacked") { |
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220 do.call(gridExtra::grid.arrange, c(plots, list(nrow = nrow, ncol = ncol))) |
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221 } |
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222 |
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223 i <- last + 1 |
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224 } |
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225 } else if (subtype %in% c("together", "diffmean", "diffmedian", "diffwith")) { |
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226 # TOGHETER or DIFFMEAN or DIFFMEDIAN or DIFFWITH =============== |
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227 |
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228 rainbow_colors <- grDevices::rainbow(n) |
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229 |
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230 if (createWindow) { |
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231 grDevices::dev.new(noRStudioGD = TRUE) |
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232 } |
2
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233 graphics::par(mfrow = c(nrow, ncol)) |
7
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234 |
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235 plots <- list() |
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236 |
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237 # Loop for Re, Im, Mod and Arg |
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238 for (name in names(elements)) { |
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239 # Get this part of the signal |
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240 element <- elements[[name]] |
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241 |
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242 # Express the signal according to a reference if asked by `subtype' |
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243 if (subtype == "diffmean") { |
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244 element <- sweep(element, MARGIN = 2, colMeans(element), `-`) |
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245 } else if (subtype == "diffmedian") { |
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246 element <- sweep(element, MARGIN = 2, matrixStats::colMedians(element), `-`) |
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247 } else if (subtype == "diffwith") { |
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248 element <- sweep(element, MARGIN = 2, element[row, ], `-`) |
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249 if (row == 1 & n > 1) { |
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250 # Since we use plot on the first row and lines on the following, the y |
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251 # scale is calculated at the first row so if the first row is all 0, it |
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252 # causes problems |
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253 tmp <- element[1, ] |
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254 element[1, ] <- element[2, ] |
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255 element[2, ] <- tmp |
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256 } |
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257 } |
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258 melted <- reshape2::melt(elements[[name]][i:last, ], varnames = c("rowname", "Var")) |
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259 |
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260 plots[[name]] <- ggplot2::ggplot(melted, ggplot2::aes( |
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261 x = Var, |
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262 y = value, group = rowname, colour = rowname |
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263 )) + |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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264 ggplot2::geom_line() + |
122df1bf0a8c
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265 ggplot2::labs(x = xlab, y = name) + |
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266 ggplot2::scale_colour_discrete(name = NULL) + |
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267 ggplot2::ggtitle(main) |
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268 |
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269 if ((melted[1, "Var"] - melted[(dim(melted)[1]), "Var"]) > |
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270 0) { |
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271 plots[[name]] <- plots[[name]] + ggplot2::scale_x_reverse() |
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272 } |
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273 |
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274 do.call(gridExtra::grid.arrange, c(plots, list( |
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275 nrow = nrow, |
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276 ncol = ncol |
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277 ))) |
2
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278 } |
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279 } |
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280 } |