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piemap.R

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+if (!require("getopt")) install.packages("getopt")
+spec <- matrix(c(
+        'input', 'i', 1, 'character',
+        'output', 'o', 1, 'character',
+        'help', 'h', 0, 'logical'
+        ), byrow = TRUE, ncol = 4)
+opt <- getopt(spec)
+
+print_usage <- function(spec = NULL) {
+        getopt(spec, usage = TRUE)
+        cat('
+Example:
+1) Rscript map.R -i [map.data] -o [output_file_name]
+2) Rscript amp.R --input [map.data] --output [output_file_name]
+The format of input file:
+Latitude	Longitude	sample1	sample2	sample3
+-38.416097	-63.616672      1       0       4
+-35.675147	-71.542969      0       0       0
+-32.522779	-55.765835      1       0       2
+\n')
+        q('no')
+}
+if (!is.null(opt$help)) print_usage(spec)
+library (rworldmap)
+library(rworldxtra)
+
+pdf(paste(opt$output, 'pdf', sep = '.'),height=10, width=20)
+color_list <-c('gray3','plum1','peru','olivedrab2','firebrick1','grey70','dodgerblue','gold1','hotpink2','orchid','cornsilk')
+mapdata <- read.table(opt$input, head=T,sep='\t',)
+mapdata  <- as.data.frame(mapdata)
+class <- names(mapdata)[-1][-1] #delete "Longitude" and  "Latitude"
+random_col <- sample(color_list,size=length(class)) #select color
+
+mapPies(mapdata,nameX="Longitude",nameY="Latitude",nameZs=class,mapRegion='world',symbolSize=1.3,barOrient='vert',oceanCol="grey",landCol="white",addCatLegend=F,zColours =random_col)
+dev.off()