Mercurial > repos > agpetit > calculate_diameter

annotate visualize_pore_diameter_aqp.R @ 10:afd0260e676f draft

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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 3111e03da3d8644ceaf94e9796f6c4206d3fe440-dirty"
author agpetit
date Tue, 07 Jun 2022 12:04:45 +0000
parents e5cf7698a2af
children f5064c93f7ab
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c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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1 #!/usr/bin/env Rscript
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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agpetit
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3 # install and/or load necessary packages
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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4 useful_packages <- c("conflicted", "getopt", "tidyverse", "ggplot2", "ggpubr")
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agpetit
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5 uninstalled_packages <- setdiff(useful_packages, rownames(installed.packages()))
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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6 invisible(lapply(useful_packages, require, character.only = TRUE, warn.conflicts = TRUE, quietly = TRUE))
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7
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8 spec <- matrix(c(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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9 "input_file", "i", 1, "character",
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10 "aqp_distribution", "a", 2, "logical",
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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11 "protomer_distribution", "p", 2, "logical",
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12 "all_distribution", "d", 2, "logical",
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13 "pdf", "f", 2, "logical"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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14 ), byrow = TRUE, ncol = 4)
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15 opt <- getopt(spec)
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17 if (is.null(opt$input_file)) {
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18 print("A file containing an array must be given as input with the -f argument")
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19 quit(status = 1)
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20 }
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22 if (is.null(opt$aqp_distribution)) {
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23 opt$aqp_distribution <- TRUE
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24 }
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25
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26 if (is.null(opt$protomer_distribution)) {
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agpetit
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27 opt$protomer_distribution <- TRUE
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28 }
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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29
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30 if (is.null(opt$all_distribution)) {
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31 opt$all_distribution <- TRUE
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32 }
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33
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34 if (is.null(opt$pdf)) {
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35 opt$pdf <- TRUE
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36 }
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37
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38 tibble_sort <- read.delim(opt$input_file)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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39 tibble_sort <- as_tibble(tibble_sort)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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40 colnames(tibble_sort) <- colnames(tibble_sort) %>%
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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41 as_tibble() %>%
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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42 mutate(value = str_replace_all(value, "\\.", "_"), value = gsub("_+Angstroms_", "", value), value = str_replace(value, "Time__ps_", "time"), value = str_replace(value, "_", "."), value = str_replace(value, "_", ".")) %>%
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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43 unlist()
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44 tibble_sort$time <- as.numeric(gsub("-[0-9]+.[0-9]+", "", tibble_sort$time))
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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45
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46 tibble_sort_mean <- tibble_sort[, 1:9]
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47 tibble_sort_std <- tibble_sort[, c(1, 10:17)]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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48 colnames(tibble_sort_mean) <- gsub("_mean", "", colnames(tibble_sort_mean))
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49 colnames(tibble_sort_std) <- gsub("_std", "", colnames(tibble_sort_std))
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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50
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51 tibble_sort_mean_long <- tibble_sort_mean %>%
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52 pivot_longer(cols = contains("AQP"), values_to = "distance") %>%
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agpetit
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53 separate(name, into = c("aqp", "protomer", "Couple"), sep = "[.]") %>%
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54 mutate(protomer = str_replace(protomer, "P", "Protomer "))
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55
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56 tibble_sort_std_long <- tibble_sort_std %>%
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57 pivot_longer(cols = contains("AQP"), values_to = "distance") %>%
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58 separate(name, into = c("aqp", "protomer", "Couple"), sep = "[.]") %>%
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59 mutate(protomer = str_replace(protomer, "P", "Protomer "))
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60
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61 create_ggplot <- function(tibble_mean, tibble_std, group, color, wrap, title) {
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62 tibble_mean_distance <- tibble_mean %>%
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63 group_by_at(group) %>%
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64 summarise(mean_distance = (mean(distance)))
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65 tibble_std_distance <- tibble_std %>%
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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66 group_by_at(group) %>%
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67 summarise(std_distance = (mean(distance)))
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68 tibble_mean_std_distance <- inner_join(tibble_mean_distance, tibble_std_distance, by = group)
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69 g_distribution <- ggplot(tibble_mean_std_distance, aes(x = time / 1000, y = mean_distance)) +
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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70 geom_line(aes(color = .data[[color]])) +
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71 geom_ribbon(aes(ymin = mean_distance - std_distance, ymax = mean_distance
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agpetit
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72 + std_distance, fill = .data[[color]]), alpha = 0.3) +
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73 facet_wrap(wrap, nrow = 2) + theme(legend.position = "top") + guides(color = "none", fill = "none") +
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74 ggtitle(label = title, subtitle = "The envelope represents the standard deviation.") +
2
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75 ylab(label = "ArR-ArR distance (Ångströms)") + xlab(label = "Time (ns)")
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76 return(g_distribution)
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77 }
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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78
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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79 list_ggplot <- list()
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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parents:
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80
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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81 if (opt$aqp_distribution == TRUE) {
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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82 group_aqp <- c("time", "aqp")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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83 color_aqp <- "aqp"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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84 wrap_aqp <- c("aqp")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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85 title_aqp <- "Average distance ArR-ArR by AQP (4 protomers)"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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86 g_aqp_distribution <- create_ggplot(tibble_sort_mean_long, tibble_sort_std_long, group_aqp, color_aqp, wrap_aqp, title_aqp)
9
e5cf7698a2af "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 434f3e872798e786f0c6a88939455692f711496c"
agpetit
parents: 2
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87 ggsave("Distance_distribution_by_aquaporin.png", g_aqp_distribution, width = 40, height = 20, units = "cm")
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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88 list_ggplot[[1]] <- g_aqp_distribution
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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89 }
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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90
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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91 if (opt$protomer_distribution == TRUE) {
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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92 group_protomer <- c("time", "protomer")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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93 color_protomer <- "protomer"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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94 wrap_protomer <- c("protomer")
9
e5cf7698a2af "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 434f3e872798e786f0c6a88939455692f711496c"
agpetit
parents: 2
diff changeset
95 title_protomer <- "Average distance ArR-ArR by protomer (2 aquaporins)"
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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96 g_protomer_distribution <- create_ggplot(tibble_sort_mean_long, tibble_sort_std_long, group_protomer, color_protomer, wrap_protomer, title_protomer)
9
e5cf7698a2af "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 434f3e872798e786f0c6a88939455692f711496c"
agpetit
parents: 2
diff changeset
97 ggsave("Distance_distribution_by_protomer.png", g_protomer_distribution, width = 40, height = 20, units = "cm")
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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98 list_ggplot[[2]] <- g_protomer_distribution
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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99 }
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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parents:
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100
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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101 if (opt$all_distribution == TRUE) {
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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102 group_all <- c("time", "aqp", "protomer")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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103 color_all <- "protomer"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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104 wrap_all <- c("aqp", "protomer")
10
afd0260e676f "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 3111e03da3d8644ceaf94e9796f6c4206d3fe440-dirty"
agpetit
parents: 9
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105 title_all <- "Average distance ArR-ArR by protomer and AQP"
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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106 g_all_distribution <- create_ggplot(tibble_sort_mean_long, tibble_sort_std_long, group_all, color_all, wrap_all, title_all)
9
e5cf7698a2af "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 434f3e872798e786f0c6a88939455692f711496c"
agpetit
parents: 2
diff changeset
107 ggsave("Distance_distribution_on_all_protomers.png", g_all_distribution, width = 40, height = 20, units = "cm")
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
108 list_ggplot[[3]] <- g_all_distribution
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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109 }
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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110
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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111 if (opt$pdf == TRUE) {
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e5cf7698a2af "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 434f3e872798e786f0c6a88939455692f711496c"
agpetit
parents: 2
diff changeset
112 ggexport(list_ggplot, filename = "all_graphics_distribution.pdf", width = 18, heigh = 18)
10
afd0260e676f "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 3111e03da3d8644ceaf94e9796f6c4206d3fe440-dirty"
agpetit
parents: 9
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113 }