Mercurial > repos > ecology > bar_plot
diff Map_shp.R @ 0:985f8839aebd draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
author | ecology |
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date | Sat, 25 Nov 2023 15:18:01 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Map_shp.R Sat Nov 25 15:18:01 2023 +0000 @@ -0,0 +1,62 @@ +library(ggplot2) +library(sf) +library(dplyr) +library(RColorBrewer) +library(ggspatial) + +args = commandArgs(trailingOnly=TRUE) +if (length(args)==0) +{ + stop("This tool needs at least one argument") +}else{ + dataMap <- args[1] + dataEvo <- args[2] + title <- args[3] + legend <- args[4] + coord <- args[5] + +} + +title <- gsub("\\\\n", "\n", title) +legend <-gsub("\\\\n", "\n", legend) +#read data + +data_map = st_read(dataMap) +data_evo = read.delim(dataEvo,header=TRUE,sep="\t") + +#bring together data + +data_fin = bind_cols(data_map,data_evo[2]) + + +# define the data intervals +intervals <- cut(data_fin$Evolution_rate, breaks = c(-Inf, 0, 9, 20, Inf), labels = c("Moins de 0", "0 à 10", "10 à 20", "Plus de 20")) + +# Make the map with ggplot2 + +if (coord == "true"){ + ggplot(data_fin) + + geom_sf(aes(fill = intervals)) + + scale_fill_manual(values = c('#D9F0D3',"#A6DBA0","#5AAE61","#1B7837")) + + labs(title = title, fill = legend) + + annotation_scale() + + #outuput + ggsave("map.pdf", device = "pdf") + +}else{ + ggplot(data_fin) + + geom_sf(aes(fill = intervals)) + + scale_fill_manual(values = c('#D9F0D3',"#A6DBA0","#5AAE61","#1B7837")) + + labs(title = title, fill = legend) + + theme_void()+ + annotation_scale() + + #outuput + ggsave("map.pdf", device = "pdf") +} + + + + +