diff Bar_plot.R @ 0:985f8839aebd draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Bar_plot.R	Sat Nov 25 15:18:01 2023 +0000
@@ -0,0 +1,52 @@
+#Script pour bar plot simple 
+
+#### loading required R libraries
+#### chargement des packages R utilisés
+library(ggplot2)
+
+###### overall parameters and settings
+###### paramètres globaux utilisés
+
+args = commandArgs(trailingOnly=TRUE) 
+if (length(args)==0)
+{
+    stop("This tool needs at least one argument")
+}else{
+    data <- args[1]
+    title <- as.character(args[2])
+    error_bar <- args[3]
+    color <- as.character(args[4])
+    ylab <- as.character(args[5])
+}
+
+histo_data = read.table(data, header= T)
+
+if (error_bar == "true"){
+
+   ggplot(histo_data, aes(x = variable_name, y = variable, fill = variable_name)) +
+     geom_bar(stat = "identity", position = "dodge", fill = color) +
+     geom_errorbar(aes(ymin = variable - standard_deviation, ymax = variable + standard_deviation), 
+                   position = position_dodge(0.9), width = 0.25) +
+     geom_text(aes(label = variable), vjust = -2, color = "black", size = 4) +
+     ggtitle(title) +
+     ylab(ylab) +
+     theme_minimal()+
+     theme(legend.position = "none",
+           axis.title.x = element_blank())
+
+   ggsave("bar_plot.pdf", device = pdf, width = 20, height = 20, units = "cm")
+
+}else{
+
+   ggplot(histo_data, aes(x = variable_name, y = variable, fill = variable_name)) +
+     geom_bar(stat = "identity", position = "dodge", fill = color) +
+     geom_text(aes(label = variable), vjust = -1, color = "black", size = 4) +
+     ggtitle(title) +
+     ylab(ylab) +
+     theme_minimal()+
+     theme(legend.position = "none",
+           axis.title.x = element_blank())
+
+   ggsave("bar_plot.pdf", device = pdf, width = 20, height = 20, units = "cm")}
+
+