Different Recommendation Sites for PLOS Biology Articles

# code for figure 5: Venn diagram F1000 vs. Wikipedia for PLOS Biology articles

# load required libraries
library("plyr")
library("VennDiagram")

# load May 20, 2013 ALM report
alm <- read.csv("../data/alm_report_plos_biology_2013-05-20.csv", stringsAsFactors=FALSE)

# only look at research articles
alm <- subset(alm, alm$article_type == "Research Article")

# group articles based on values in Wikipedia and F1000
reassignWikipedia<- function(x) if (x > 0) 1 else 0
alm$wikipedia_bin <- aaply(alm$wikipedia, 1, reassignWikipedia)
reassignF1000 <- function(x) if (x > 0) 2 else 0
alm$f1000_bin <- aaply(alm$f1000, 1, reassignF1000)
alm$article_group = alm$wikipedia_bin + alm$f1000_bin
reassignCombined <- function(x) if (x == 3) 1 else 0
alm$combined_bin <- aaply(alm$article_group, 1, reassignCombined)
reassignNo <- function(x) if (x == 0) 1 else 0
alm$no_bin <- aaply(alm$article_group, 1, reassignNo)

# remember to divide f1000_bin by 2, as this is the default value
summary <- colSums(subset(alm, select=c("wikipedia_bin","f1000_bin","combined_bin","no_bin")), na.rm=TRUE)
rows <- nrow(alm)

# options
plos.colors <- c("#c9c9c7","#0000ff","#ff0000")

# plot the chart
opar <- par(mai=c(0.5,.75,3.5,0.5), omi=c(0.5,0.5,1.5,0.5), mgp=c(3,.5,.5), fg="black", cex.main=2, cex.lab=1.5, col=plos.color, col.main=plos.color, col.lab=plos.color, xaxs="i", yaxs="i")

venn.plot <- draw.triple.venn(area1=rows,area2=summary[1],area3=summary[2]/2,n12=summary[1],n23=summary[3],n13=summary[2]/2,n123=summary[3],euler.d=TRUE,scaled=TRUE,fill=plos.colors,cex=2,fontfamily = rep("sans", 7))

par(opar)