提交: 93e1937824e3d001eb4dedfa6d1082d27424d41c - myprojects-hg-reborn (hg)

Commit MetaInfo

• 修订版: 93e1937824e3d001eb4dedfa6d1082d27424d41c (tree)
• 时间: 2011-11-19 19:51:09
• 作者: lorenzo
• Commiter: lorenzo

Log Message

Some small modifications to the script that is now using faceting to explore
the data and generate panels.

更改概述

• modified: R-codes/aggregate-miscellanea.R

差异

diff -r 3e092578fed8 -r 93e1937824e3 R-codes/aggregate-miscellanea.R
--- a/R-codes/aggregate-miscellanea.R	Sat Nov 19 10:49:51 2011 +0000
+++ b/R-codes/aggregate-miscellanea.R	Sat Nov 19 10:51:09 2011 +0000
@@ -6,9 +6,16 @@
 data$aggregate <- as.factor(data$aggregate)
 
 
+n_dis <- 6 #the number of neighbors is calculated for 6
+#distances
+
+n_mon <- 8 # monomer in each aggregate
+
+plot_individual <- 0
 
 
-
+distance <- seq(1,2.25,by=0.25) #distances to calculate number
+            #neighbors
 
 qs <- ddply(data, "aggregate", function(df)
   quantile(df$eta, c(0.05, 0.25, 0.5, 0.75, 0.95)))
@@ -105,4 +112,359 @@
 
 tools::texi2dvi(fn,pdf=T)
 
+#########################################
+
+if (plot_individual==1){
+
+
+b <- ggplot(data, aes(x=X1, y=eta)) +
+           opts( panel.background=theme_rect(fill='white',
+                   size=1.5))+
+  opts(panel.grid.minor = theme_blank())+
+opts(panel.grid.major = theme_blank())+
+      opts(axis.ticks = theme_segment(colour = "black", size=1),
+           axis.ticks.length = unit(0.15, "cm"))+
+
+geom_point(size=2)+
+facet_grid(~ aggregate)+
+  xlab("Number of Neighbors at distance 1")+
+  ylab("Shielding Factor $\\eta_i$")+
+  opts(axis.title.x = theme_text(size = 20))+
+  opts(axis.title.y = theme_text(size = 20, angle=90))+
+  ## opts(axis.text.x = theme_text(size=15, colour="gray",vjust=1))+
+  ## opts(axis.text.y = theme_text(size=15, colour="gray", hjust=1))
+  opts(axis.text.x = theme_text(size=15, colour="black",vjust=1))+
+  opts(axis.text.y = theme_text(size=15, colour="black", hjust=1))
+
+
+fn <-'correlation1.tex' 
+
+tikz(fn, standAlone = TRUE, width=13,height=5)
+
+
+print(b)
+dev.off()
+
+tools::texi2dvi(fn,pdf=T)
+
+
+
+b <- ggplot(data, aes(x=X1.25, y=eta)) +
+           opts( panel.background=theme_rect(fill='white',
+                   size=1.5))+
+  opts(panel.grid.minor = theme_blank())+
+opts(panel.grid.major = theme_blank())+
+      opts(axis.ticks = theme_segment(colour = "black", size=1),
+           axis.ticks.length = unit(0.15, "cm"))+
+
+geom_point(size=2)+
+facet_grid(~ aggregate)+
+  xlab("Number of Neighbors at distance 1")+
+  ylab("Shielding Factor $\\eta_i$")+
+  opts(axis.title.x = theme_text(size = 20))+
+  opts(axis.title.y = theme_text(size = 20, angle=90))+
+  ## opts(axis.text.x = theme_text(size=15, colour="gray",vjust=1))+
+  ## opts(axis.text.y = theme_text(size=15, colour="gray", hjust=1))
+  opts(axis.text.x = theme_text(size=15, colour="black",vjust=1))+
+  opts(axis.text.y = theme_text(size=15, colour="black", hjust=1))
+
+
+fn <-'correlation125.tex' 
+
+tikz(fn, standAlone = TRUE, width=13,height=5)
+
+
+print(b)
+dev.off()
+
+tools::texi2dvi(fn,pdf=T)
+
+
+
+
+
+b <- ggplot(data, aes(x=X1, y=eta)) +
+           opts( panel.background=theme_rect(fill='white',
+                   size=1.5))+
+  opts(panel.grid.minor = theme_blank())+
+opts(panel.grid.major = theme_blank())+
+      opts(axis.ticks = theme_segment(colour = "black", size=1),
+           axis.ticks.length = unit(0.15, "cm"))+
+
+geom_point(size=2)+
+facet_grid(~ aggregate)+
+  xlab("Number of Neighbors at distance 1.5")+
+  ylab("Shielding Factor $\\eta_i$")+
+  opts(axis.title.x = theme_text(size = 20))+
+  opts(axis.title.y = theme_text(size = 20, angle=90))+
+  ## opts(axis.text.x = theme_text(size=15, colour="gray",vjust=1))+
+  ## opts(axis.text.y = theme_text(size=15, colour="gray", hjust=1))
+  opts(axis.text.x = theme_text(size=15, colour="black",vjust=1))+
+  opts(axis.text.y = theme_text(size=15, colour="black", hjust=1))
+
+
+fn <-'correlation150.tex' 
+
+tikz(fn, standAlone = TRUE, width=13,height=5)
+
+
+print(b)
+dev.off()
+
+tools::texi2dvi(fn,pdf=T)
+
+
+
+b <- ggplot(data, aes(x=X1.75, y=eta)) +
+           opts( panel.background=theme_rect(fill='white',
+                   size=1.5))+
+  opts(panel.grid.minor = theme_blank())+
+opts(panel.grid.major = theme_blank())+
+      opts(axis.ticks = theme_segment(colour = "black", size=1),
+           axis.ticks.length = unit(0.15, "cm"))+
+
+geom_point(size=2)+
+facet_grid(~ aggregate)+
+  xlab("Number of Neighbors at distance 1")+
+  ylab("Shielding Factor $\\eta_i$")+
+  opts(axis.title.x = theme_text(size = 20))+
+  opts(axis.title.y = theme_text(size = 20, angle=90))+
+  ## opts(axis.text.x = theme_text(size=15, colour="gray",vjust=1))+
+  ## opts(axis.text.y = theme_text(size=15, colour="gray", hjust=1))
+  opts(axis.text.x = theme_text(size=15, colour="black",vjust=1))+
+  opts(axis.text.y = theme_text(size=15, colour="black", hjust=1))
+
+
+fn <-'correlation175.tex' 
+
+tikz(fn, standAlone = TRUE, width=13,height=5)
+
+
+print(b)
+dev.off()
+
+tools::texi2dvi(fn,pdf=T)
+
+
+
+b <- ggplot(data, aes(x=X2, y=eta)) +
+           opts( panel.background=theme_rect(fill='white',
+                   size=1.5))+
+  opts(panel.grid.minor = theme_blank())+
+opts(panel.grid.major = theme_blank())+
+      opts(axis.ticks = theme_segment(colour = "black", size=1),
+           axis.ticks.length = unit(0.15, "cm"))+
+
+geom_point(size=2)+
+facet_grid(~ aggregate)+
+  xlab("Number of Neighbors at distance 1")+
+  ylab("Shielding Factor $\\eta_i$")+
+  opts(axis.title.x = theme_text(size = 20))+
+  opts(axis.title.y = theme_text(size = 20, angle=90))+
+  ## opts(axis.text.x = theme_text(size=15, colour="gray",vjust=1))+
+  ## opts(axis.text.y = theme_text(size=15, colour="gray", hjust=1))
+  opts(axis.text.x = theme_text(size=15, colour="black",vjust=1))+
+  opts(axis.text.y = theme_text(size=15, colour="black", hjust=1))
+
+
+fn <-'correlation200.tex' 
+
+tikz(fn, standAlone = TRUE, width=13,height=5)
+
+
+print(b)
+dev.off()
+
+tools::texi2dvi(fn,pdf=T)
+
+
+
+b <- ggplot(data, aes(x=X2.25, y=eta)) +
+           opts( panel.background=theme_rect(fill='white',
+                   size=1.5))+
+  opts(panel.grid.minor = theme_blank())+
+opts(panel.grid.major = theme_blank())+
+      opts(axis.ticks = theme_segment(colour = "black", size=1),
+           axis.ticks.length = unit(0.15, "cm"))+
+
+geom_point(size=2)+
+facet_grid(~ aggregate)+
+  xlab("Number of Neighbors at distance 1")+
+  ylab("Shielding Factor $\\eta_i$")+
+  opts(axis.title.x = theme_text(size = 20))+
+  opts(axis.title.y = theme_text(size = 20, angle=90))+
+  ## opts(axis.text.x = theme_text(size=15, colour="gray",vjust=1))+
+  ## opts(axis.text.y = theme_text(size=15, colour="gray", hjust=1))
+  opts(axis.text.x = theme_text(size=15, colour="black",vjust=1))+
+  opts(axis.text.y = theme_text(size=15, colour="black", hjust=1))
+
+
+fn <-'correlation225.tex' 
+
+tikz(fn, standAlone = TRUE, width=13,height=5)
+
+
+print(b)
+dev.off()
+
+tools::texi2dvi(fn,pdf=T)
+
+
+}
+
+################################################
+
+#time to generate a new data set for a better faceting plot
+
+n_agg <- length(levels(data$aggregate))
+
+agg_label <- c()
+nei_dist <- c()
+number_nei <- c()
+eta_long <- c()
+
+
+ld <- length(distance)
+
+
+for (i in seq(n_agg)){
+
+for (m in seq(ld)){
+
+temp <- rep(distance[m], n_mon)
+nei_dist <- c(nei_dist,temp)
+  
+
+}
+
+
+
+}
+
+for (i in seq(n_agg)){
+
+agg_label <- c(agg_label,rep(i,n_mon*ld))
+
+#nei_dist <- c(nei_dist,rep(distance,n_mon))
+
+#number_nei <- c(number_nei, )
+
+sel <- which(data$aggregate==i)
+
+data_temp <- data[sel,3:(3+ld-1)]
+
+data_temp <- as.matrix(data_temp)
+dim(data_temp) <- c(ld*n_mon,1)
+
+number_nei <- c(number_nei,data_temp)
+
+
+
+
+eta_long <- c(eta_long,rep(data$eta[sel],length(distance)))
+
+
+}
+
+
+data_new <- cbind(eta_long, agg_label,nei_dist,number_nei )                               
+data_new <- as.data.frame(data_new)
+
+
+names(data_new) <- c("eta","aggregate_number",
+                     "distance", "number_nei")
+
+data_new$aggregate_number<-as.factor(data_new$aggregate_number)
+data_new$distance<-as.factor(data_new$distance)
+
+
+b <- ggplot(data_new, aes(x=number_nei, y=eta)) +
+           opts( panel.background=theme_rect(fill='white',
+                   size=1.5))+
+  opts(panel.grid.minor = theme_blank())+
+opts(panel.grid.major = theme_blank())+
+      opts(axis.ticks = theme_segment(colour = "black", size=1),
+           axis.ticks.length = unit(0.15, "cm"))+
+
+geom_point(size=2)+
+facet_grid(distance~ aggregate_number)+
+  xlab("Number of neighbors inside the shell")+
+  ylab("Shielding Factor $\\eta_i$")+
+  opts(axis.title.x = theme_text(size = 20))+
+  opts(axis.title.y = theme_text(size = 20, angle=90))+
+  ## opts(axis.text.x = theme_text(size=15, colour="gray",vjust=1))+
+  ## opts(axis.text.y = theme_text(size=15, colour="gray", hjust=1))
+  opts(axis.text.x = theme_text(size=15, colour="black",vjust=1))+
+  opts(axis.text.y = theme_text(size=15, colour="black", hjust=1))
+
+
+fn <-'correlation_total.tex' 
+
+tikz(fn, standAlone = TRUE, width=15,height=15)
+
+
+print(b)
+dev.off()
+
+tools::texi2dvi(fn,pdf=T)
+
+
+##########################à
+
+b <- ggplot(data_new, aes(x=number_nei, y=eta)) +
+           opts( panel.background=theme_rect(fill='white',
+                   size=1.5))+
+  opts(panel.grid.minor = theme_blank())+
+opts(panel.grid.major = theme_blank())+
+      opts(axis.ticks = theme_segment(colour = "black", size=1),
+           axis.ticks.length = unit(0.15, "cm"))+
+
+geom_point(size=2)+
+facet_grid( ~ distance)+
+  xlab("Number of neighbors inside the shell")+
+  ylab("Shielding factor $\\eta_i$")+
+  opts(axis.title.x = theme_text(size = 20))+
+  opts(axis.title.y = theme_text(size = 20, angle=90))+
+  ## opts(axis.text.x = theme_text(size=15, colour="gray",vjust=1))+
+  ## opts(axis.text.y = theme_text(size=15, colour="gray", hjust=1))
+  opts(axis.text.x = theme_text(size=15, colour="black",vjust=1))+
+  opts(axis.text.y = theme_text(size=15, colour="black", hjust=1))
+
+
+fn <-'correlation_total_aggregates_together.tex' 
+
+tikz(fn, standAlone = TRUE, width=15,height=5)
+
+
+print(b)
+dev.off()
+
+tools::texi2dvi(fn,pdf=T)
+
+
+####################################################
+
+cor_data <- seq(ld)
+
+for (i in seq(ld)){
+
+sel <- which(data_new$distance==distance[i])
+
+my_corr <- cor(data_new$eta[sel],data_new$number_nei[sel])
+
+cor_data[i] <- my_corr
+
+
+}
+
+
+cor_data <- abs(cor_data)
+
+print ("cor_data is, ")
+print(cor_data)
+
+
+write.csv(cor_data,"correlation_data.csv", row.names=FALSE)
+
+
 print("So far so good")