Merge branch 'master' of https://github.com/UBOdin/EttuBench

UBOdin · Nov 16, 2017 · ca4445b · ca4445b
2 parents 3897b6f + 57bfbdd
commit ca4445b
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Showing 14 changed files with 570 additions and 57 deletions.
diff --git a/.Rhistory b/.Rhistory
diff --git a/figure/compare_betacv.pdf b/figure/compare_betacv.pdf
diff --git a/figure/compare_dunn.pdf b/figure/compare_dunn.pdf
diff --git a/figure/compare_silhouette.pdf b/figure/compare_silhouette.pdf
diff --git a/figure/module.pdf b/figure/module.pdf
diff --git a/figure/sil_bombay_Aligon.pdf b/figure/sil_bombay_Aligon.pdf
diff --git a/figure/sil_bombay_Aligon_regularization.pdf b/figure/sil_bombay_Aligon_regularization.pdf
diff --git a/figure/sil_googleplus_Aligon.pdf b/figure/sil_googleplus_Aligon.pdf
diff --git a/figure/sil_googleplus_Aligon_regularization.pdf b/figure/sil_googleplus_Aligon_regularization.pdf
diff --git a/figure/sil_ub_Aligon.pdf b/figure/sil_ub_Aligon.pdf
diff --git a/figure/sil_ub_Aligon_regularization.pdf b/figure/sil_ub_Aligon_regularization.pdf
diff --git a/script_figure_2.R b/script_figure_2.R
@@ -1,36 +1,30 @@
 # set working directory
 #setwd("~/Downloads/EttuBench")
 
-# load two files evaluation.R and utils.R
-source(file = "./evaluation.R")
-source(file = "./utils.R")
-
 # load supporting libraries
-library(cluster)
-library(factoextra)
-library(RColorBrewer)
-
-dataset <- read.csv(file = "./data/bombay_queries.csv", header = TRUE, sep = "\t")
-
-distMat <- readDistMat("./data/bombay_aligon.csv")
-silhouettePlot(distMat, dataset$label, "./figure/sil_bombay_Aligon.pdf")
-
-distMat <- readDistMat("./data/bombay_aligon_regularization.csv")
-silhouettePlot(distMat, dataset$label, "./figure/sil_bombay_Aligon_regularization.pdf")
-
-dataset <- read.csv(file = "./data/ub_queries.csv", header = TRUE, sep = "\t")
-
-distMat <- readDistMat("./data/ub_aligon.csv")
-silhouettePlot(distMat, dataset$label, "./figure/sil_ub_Aligon.pdf")
-
-distMat <- readDistMat("./data/ub_aligon_regularization.csv")
-silhouettePlot(distMat, dataset$label, "./figure/sil_ub_Aligon_regularization.pdf")
-
-dataset <- read.csv(file = "./data/googleplus_queries.csv", header = TRUE, sep = "\t")
-
-distMat <- readDistMat("./data/googleplus_aligon.csv")
-silhouettePlot(distMat, dataset$label, "./figure/sil_googleplus_Aligon.pdf")
-
-distMat <- readDistMat("./data/googleplus_aligon_regularization.csv")
-silhouettePlot(distMat, dataset$label, "./figure/sil_googleplus_Aligon_regularization.pdf")
+library(ggplot2)
+
+comparison <- read.csv(file = "./data/result.csv", header = TRUE)
+comparison$dataset <- factor(comparison$dataset, 
+                             levels = c("IIT Bombay Dataset", 
+                                        "UB Exam Dataset", 
+                                        "PocketData-Google+"))
+
+ggplot(data = comparison, aes(x = metric, y = silhouette, fill = regularization)) + 
+  geom_bar(position="dodge", stat="identity") + facet_grid(~ dataset) + 
+  ylab("Average Silhouette Coefficient") + xlab("Metric") + 
+  theme_bw(base_size = 18) + theme(legend.position = "top") + scale_fill_grey() +
+  ggsave(filename = "./figure/compare_silhouette.pdf", height = 5)
+
+ggplot(data = comparison, aes(x = metric, y = beta_cv, fill = regularization)) + 
+  geom_bar(position="dodge", stat="identity") + facet_grid(~ dataset) + 
+  ylab("BetaCV") + xlab("Metric") + 
+  theme_bw(base_size = 18) + theme(legend.position = "top") + scale_fill_grey() +
+  ggsave(filename = "./figure/compare_betacv.pdf", height = 5)
+
+ggplot(data = comparison, aes(x = metric, y = dunn, fill = regularization)) + 
+  geom_bar(position="dodge", stat="identity") + facet_grid(~ dataset) + 
+  ylab("Dunn Index") + xlab("Metric") + 
+  theme_bw(base_size = 18) + theme(legend.position = "top") + scale_fill_grey() +
+  ggsave(filename = "./figure/compare_dunn.pdf", height = 5)
 
diff --git a/script_figure_3.R b/script_figure_3.R
@@ -1,29 +1,36 @@
 # set working directory
 #setwd("~/Downloads/EttuBench")
 
+# load two files evaluation.R and utils.R
+source(file = "./evaluation.R")
+source(file = "./utils.R")
+
 # load supporting libraries
-library(ggplot2)
-
-comparison <- read.csv(file = "./data/result.csv", header = TRUE)
-comparison$dataset <- factor(comparison$dataset, 
-                             levels = c("IIT Bombay Dataset", 
-                                        "UB Exam Dataset", 
-                                        "PocketData-Google+"))
-
-ggplot(data = comparison, aes(x = metric, y = silhouette, fill = regularization)) + 
-  geom_bar(position="dodge", stat="identity") + facet_grid(~ dataset) + 
-  ylab("Average Silhouette Coefficient") + xlab("Metric") + 
-  theme_bw(base_size = 18) + theme(legend.position = "top") + scale_fill_grey() +
-  ggsave(filename = "./figure/compare_silhouette.pdf")
-
-ggplot(data = comparison, aes(x = metric, y = beta_cv, fill = regularization)) + 
-  geom_bar(position="dodge", stat="identity") + facet_grid(~ dataset) + 
-  ylab("Average Silhouette Coefficient") + xlab("Metric") + 
-  theme_bw(base_size = 18) + theme(legend.position = "top") + scale_fill_grey() +
-  ggsave(filename = "./figure/compare_betacv.pdf")
-
-ggplot(data = comparison, aes(x = metric, y = dunn, fill = regularization)) + 
-  geom_bar(position="dodge", stat="identity") + facet_grid(~ dataset) + 
-  ylab("Average Silhouette Coefficient") + xlab("Metric") + 
-  theme_bw(base_size = 18) + theme(legend.position = "top") + scale_fill_grey() +
-  ggsave(filename = "./figure/compare_dunn.pdf")
+library(cluster)
+library(factoextra)
+library(RColorBrewer)
+
+dataset <- read.csv(file = "./data/bombay_queries.csv", header = TRUE, sep = "\t")
+
+distMat <- readDistMat("./data/bombay_aligon.csv")
+silhouettePlot(distMat, dataset$label, "./figure/sil_bombay_Aligon.pdf")
+
+distMat <- readDistMat("./data/bombay_aligon_regularization.csv")
+silhouettePlot(distMat, dataset$label, "./figure/sil_bombay_Aligon_regularization.pdf")
+
+dataset <- read.csv(file = "./data/ub_queries.csv", header = TRUE, sep = "\t")
+
+distMat <- readDistMat("./data/ub_aligon.csv")
+silhouettePlot(distMat, dataset$label, "./figure/sil_ub_Aligon.pdf")
+
+distMat <- readDistMat("./data/ub_aligon_regularization.csv")
+silhouettePlot(distMat, dataset$label, "./figure/sil_ub_Aligon_regularization.pdf")
+
+dataset <- read.csv(file = "./data/googleplus_queries.csv", header = TRUE, sep = "\t")
+
+distMat <- readDistMat("./data/googleplus_aligon.csv")
+silhouettePlot(distMat, dataset$label, "./figure/sil_googleplus_Aligon.pdf")
+
+distMat <- readDistMat("./data/googleplus_aligon_regularization.csv")
+silhouettePlot(distMat, dataset$label, "./figure/sil_googleplus_Aligon_regularization.pdf")
+
diff --git a/script_figure_4.R b/script_figure_4.R
@@ -21,4 +21,4 @@ ggplot(data = comparison, aes(x = Metric, y = Silhouette, fill=Regularization))
   ylab("Average Silhouette Coefficient") + xlab("Metric") + 
   theme_bw(base_size = 14) + theme(legend.position = "top", legend.title = element_blank()) + 
   scale_fill_brewer(palette = "Dark2") +
-  ggsave(file = "./figure/module.pdf")
+  ggsave(file = "./figure/module.pdf")