Mercurial > repos > marie-tremblay-metatoul > 2dnmrannotation

annotate viridis.R @ 4:cf11fa0c47c8 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
author workflow4metabolomics
date Thu, 23 Jan 2025 15:28:44 +0000
parents 546c7ccd2ed4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
diff changeset
1 viridis <- function(n, alpha = 1, begin = 0, end = 1, direction = 1, option = "D") {
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
diff changeset
2 if (begin < 0 | begin > 1 | end < 0 | end > 1) {
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
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3 stop("begin and end must be in [0,1]")
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
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4 }
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
diff changeset
5 if (abs(direction) != 1) {
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
diff changeset
6 stop("direction must be 1 or -1")
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
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7 }
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
diff changeset
8 if (direction == -1) {
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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9 tmp <- begin
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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10 begin <- end
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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11 end <- tmp
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
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12 }
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
diff changeset
13 option <- switch(EXPR = option,
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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14 A = "A",
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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15 magma = "A",
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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16 B = "B",
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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17 inferno = "B",
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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18 C = "C",
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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19 plasma = "C",
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
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20 D = "D",
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
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21 viridis = "D",
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
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22 E = "E",
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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23 cividis = "E",
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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24 {
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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25 warning(paste0("Option '", option, "' does not exist. Defaulting to 'viridis'."))
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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26 "D"
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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27 }
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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28 )
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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29 map <- viridisLite::viridis.map[viridisLite::viridis.map$opt ==
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
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30 option, ]
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
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31 map_cols <- grDevices::rgb(map$R, map$G, map$B)
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
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32 fn_cols <- grDevices::colorRamp(map_cols,
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
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33 space = "Lab",
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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34 interpolate = "spline"
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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35 )
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
diff changeset
36 cols <- fn_cols(seq(begin, end, length.out = n)) / 255
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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37 grDevices::rgb(cols[, 1], cols[, 2], cols[, 3], alpha = alpha)
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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38 }