plot tweaks

2 files changed, 36 insertions, 19 deletions

diff --git a/R Scripts/plot-data-prep.R b/R Scripts/plot-data-prep.R
index d577b5d..937512a 100644
--- a/R Scripts/plot-data-prep.R
+++ b/R Scripts/plot-data-prep.R
@@ -8,6 +8,7 @@ library(gridExtra)
 # create bipartite graph
 edges = c(1,6,
           1,7,
+          1,10,
           2,8,
           3,7,
           3,8,
@@ -18,7 +19,7 @@ edges = c(1,6,
           5,9)
 g = graph.bipartite(c(rep(T,5),rep(F,5)),edges)
 
-par(mfrow=c(1,3))
+par(mfrow=c(1,3), mar=c(1,1,1,1))
 # (A) data table
 data = data.frame(get.edgelist(g))
 data$X2 = toupper(letters[data$X2-5])
@@ -38,21 +39,24 @@ plot(g, layout=layout[,2:1], vertex.color=cols,edge.color='black',
      vertex.label.color='white',vertex.label.family='sans')
 
 # (C) unipartite person-person graph
+par(mar=rep(1,4))
 g2 = bipartite.projection(g)$proj1
-layout.g2 = layout.auto(g2)
-plot(g2, vertex.color='#1f78b4', edge.color='black',layout=layout.g2,
+layout.g2 = matrix(c(0,.33,-.75,-.33,0,-1,0,1,.75,-.33),ncol=2,byrow=T)
+plot(g2, vertex.color='#1f78b4', edge.color='black',layout=layout.g2,rescale=F,
      vertex.frame.color=NA,vertex.size=30,vertex.label=toupper(letters[1:5]),
      vertex.label.color='white',vertex.label.family='sans')
 
-#############
+##############################################################################
+##############################################################################
 #### Hawkes Process Diagram
-par(mfrow=c(1,3))
+layout(matrix(c(1,2,3,3,3,3), ncol=2, byrow = TRUE))
 
 vics = data.frame(IC = toupper(letters[1:5]), 
                   Victim = c(T,F,F,F,T),
-                  Day = c(3,NA,NA,NA,5))
+                  Day = c(2,NA,NA,NA,4))
 colnames(vics) = c('Identity Code (IC)','Victim','Infection Date')
 
+# A
 plot.new()
 vps <- baseViewports()
 pushViewport(vps$figure)
@@ -62,28 +66,37 @@ grid.table(vics)
 cols = rep('#1f78b4',vcount(g2))
 cols[vics$Victim==T] = '#e41a1c'
 
-plot(g2, vertex.color=cols, edge.color='black',layout=layout.g2,
+# B
+plot(g2, vertex.color=cols, edge.color='black',layout=layout.g2,rescale=F,
      vertex.frame.color=NA,vertex.size=30,vertex.label=toupper(letters[1:5]),
-     vertex.label.color='white',vertex.label.family='sans')
+     vertex.label.color='white',vertex.label.family='sans',axes=F)
 
 
+# C 
+par(mar=c(5.1, 4.1, 4.1, 2.1))
 rate = function(x){
   print(x)
-  r = rep(.3,length(x))
-  times = c(1,4)
+  r = rep(base+0.3,length(x))
   for (time in times){
-    r[x>=time] = r[x>=time] + 1.5*exp((time-x[x>=time])/4)
+    r[x>=time] = r[x>=time] + 1.5*exp((time-x[x>=time])/2)
   }
   return(r)
 }
-plot(rate,from=0,to=10,ylim=c(0,3),lwd=0,bty='l',
-     yaxt='n',xlab='Date',ylab='Infection Rate')
-mtext("Date", line = 3, side = 1)
-n = 1000
-xs = c(0,seq(0,10,length.out=n),10)
-ys = rate(xs)
-ys[c(1,n+2)] = 0
-polygon(xs,ys,col='#1f78b4',border=NA)
 
+tmin = 1
+tmax = 6
+n = 1000
+plot(rate,from=tmin,to=tmax,ylim=c(0,15),lwd=0,bty='l',col='white',
+     yaxt='n',xlab='Date',ylab='Infection Rate')
+for(i in 1:vcount(g2)){
+  base <<- 3*(5-i)
+  times <<- vics[neighbors(g2,i),3]
+  times <<- times[!is.na(times)]
+  xs = c(tmin,seq(tmin,tmax,length.out=n),tmax)
+  ys = rate(xs)
+  ys[c(1,n+2)] = base
+  polygon(xs,ys,col='#1f78b4',border=NA)
+}
+axis(2, at=seq(0.3,12.3,3), lab=toupper(letters[seq(5,1,-1)]), tick=F, las=T,lwd=0)
 
 
diff --git a/R Scripts/plot-network.R b/R Scripts/plot-network.R
index 4c1f9fa..93c48fb 100644
--- a/R Scripts/plot-network.R
+++ b/R Scripts/plot-network.R
@@ -19,3 +19,7 @@ load('Results/layout.RData')
 par(bg='#e0e0e0')
 plot(lcc,vertex.size=1,vertex.color=cols,vertex.label=NA,
      layout=layout.drl,edge.color=NA,vertex.frame.color=NA)
+
+# library(rgl)
+rglplot(lcc,vertex.size=1,vertex.color=cols,vertex.label=NA,
+     layout=layout.drl,edge.color=NA,vertex.frame.color=NA)