Mercurial > repos > ecology > map_shp

annotate Bar_plot.R @ 0:ce9979488ebb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
author ecology
date Sat, 25 Nov 2023 15:18:33 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
1 #Script pour bar plot simple
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
2
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
3 #### loading required R libraries
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
4 #### chargement des packages R utilisés
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
5 library(ggplot2)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
6
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
7 ###### overall parameters and settings
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
8 ###### paramètres globaux utilisés
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
9
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
10 args = commandArgs(trailingOnly=TRUE)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
11 if (length(args)==0)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
12 {
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
13 stop("This tool needs at least one argument")
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
14 }else{
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
15 data <- args[1]
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
16 title <- as.character(args[2])
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
17 error_bar <- args[3]
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
18 color <- as.character(args[4])
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
19 ylab <- as.character(args[5])
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
20 }
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
21
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
22 histo_data = read.table(data, header= T)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
23
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
24 if (error_bar == "true"){
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
25
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
26 ggplot(histo_data, aes(x = variable_name, y = variable, fill = variable_name)) +
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
27 geom_bar(stat = "identity", position = "dodge", fill = color) +
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
28 geom_errorbar(aes(ymin = variable - standard_deviation, ymax = variable + standard_deviation),
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
29 position = position_dodge(0.9), width = 0.25) +
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
30 geom_text(aes(label = variable), vjust = -2, color = "black", size = 4) +
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
31 ggtitle(title) +
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
32 ylab(ylab) +
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
33 theme_minimal()+
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
34 theme(legend.position = "none",
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
35 axis.title.x = element_blank())
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
36
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
37 ggsave("bar_plot.pdf", device = pdf, width = 20, height = 20, units = "cm")
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
38
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
39 }else{
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
40
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
41 ggplot(histo_data, aes(x = variable_name, y = variable, fill = variable_name)) +
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
42 geom_bar(stat = "identity", position = "dodge", fill = color) +
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
43 geom_text(aes(label = variable), vjust = -1, color = "black", size = 4) +
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
44 ggtitle(title) +
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
45 ylab(ylab) +
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
46 theme_minimal()+
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
47 theme(legend.position = "none",
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
48 axis.title.x = element_blank())
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
49
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
50 ggsave("bar_plot.pdf", device = pdf, width = 20, height = 20, units = "cm")}
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
51
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
parents:
diff changeset
52