Visualize Geographical Bias between PubMed Results

Script

#Inputs:  countries (String vector)
#         counts    (Integer vector)
#
#Outputs: output (String)

library(rworldmap);
MIN_PAPERS<-3;

affiliation1<-as.data.frame(matrix(nrow=length(countries1), ncol=2));
affiliation1[,1]<-data.matrix(countries1);
affiliation1[,2]<-data.matrix(counts1)+0.31; # to be able to take logarithms
total1<-sum(counts1);

affiliation2<-as.data.frame(matrix(nrow=length(countries2), ncol=2));
affiliation2[,1]<-data.matrix(countries2);
affiliation2[,2]<-data.matrix(counts2)+0.31; # to be able to take logarithms
total2<-sum(counts2);


affiliation<-affiliation1; # copy to store ratios
affiliation[,2]<-log2((affiliation1[,2]/total1)/(affiliation2[,2]/total2));
for (i in seq(1,length(countries1))) {if((affiliation1[i,2] + affiliation2[i,2])<((MIN_PAPERS-1)+0.63)) affiliation[i,2]<-1048577};

sPDF<-joinCountryData2Map(affiliation, joinCode="ISO3", nameJoinColumn="V1");

output<-"c:/tmp/geographical_bias.pdf";
pdf(output, paper = "a4r", width = 10, height = 4);
par(mai=c(0,0,0.2,0),xaxs="i",yaxs="i");
fixed_latitude<-c(-57, 85); # do not show polar regions (not of much interest here)
fixed_longitude<-c(-100,100);
mapCountryData(sPDF, nameColumnToPlot="V2", catMethod = seq(from=-7, to=7, length.out=101), xlim=fixed_longitude, ylim=fixed_latitude, colourPalette = c("red","yellow", "green"), addLegend = TRUE, legendShrink=0.5, borderCol ='black', mapTitle ='Geographical Bias');
dev.off();

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