-
Notifications
You must be signed in to change notification settings - Fork 0
/
Rcode.R
286 lines (176 loc) · 14.1 KB
/
Rcode.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
#Installing necessarry packages
install.packages("ggplot2")
install.packages("hrbrthemes")
install.packages("car")
install.packages("dendextend")
install.packages("tidyverse")
install.packages("ggpubr")
install.packages("rstatix")
install.packages("readxl")
library(ggplot2)
library(hrbrthemes)
library(car)
library(readxl)
#Import dataset: data <- read_excel("data.xlsx")
as.factor(data$Level)
as.factor(data$Phase)
#bi-plot 4 Levels vs 2 Levels
ggplot(data, aes(x=AlFeSi, y=MgO, color=Phase)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))
ggplot(data, aes(x=AlFeSi, y=MgO, color=Level)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))
#Import dataset omitting sample #9 and #20: data2 <- read_excel("data2.xlsx")
as.factor(data2$Level)
as.factor(data2$Phase)
#bi-plot 4 Levels vs 2 Levels
ggplot(data2, aes(x=AlFeSi, y=MgO, color=Phase)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))
ggplot(data2, aes(x=AlFeSi, y=MgO, color=Level)) + geom_point(size=6) +
labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))
ggplot(data2, aes(x=AlFeSi, y=MgO, color=Phase)) + geom_boxplot() +
labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))
ggplot(data2, aes(x=AlFeSi, y=MgO, color=Level)) + geom_boxplot() +
labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))
#bi-plots according to all major elements vs Al+Fe/Si
#Na2O vs Al+Fe/Si
ggplot(data2, aes(x=AlFeSi, y=Na2O, color=Phase)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("Na"["2"] ~ "O"))
ggplot(data2, aes(x=AlFeSi, y=Na2O, color=Level)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("Na"["2"] ~ "O"))
ggplot(data2, aes(x=AlFeSi, y=Na2O, color=Phase)) + geom_boxplot() + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("Na"["2"] ~ "O"))
ggplot(data2, aes(x=AlFeSi, y=Na2O, color=Level)) + geom_boxplot() + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("Na"["2"] ~ "O"))
#P2O5 vs Al+Fe/Si
ggplot(data2, aes(x=AlFeSi, y=P2O5, color=Phase)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("P"["2"] ~ "O"["5"]))
ggplot(data2, aes(x=AlFeSi, y=P2O5, color=Level)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("P"["2"] ~ "O"["5"]))
ggplot(data2, aes(x=AlFeSi, y=P2O5, color=Phase)) + geom_boxplot() + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("P"["2"] ~ "O"["5"]))
ggplot(data2, aes(x=AlFeSi, y=P2O5, color=Level)) + geom_boxplot() + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("P"["2"] ~ "O"["5"]))
#K2O vs Al+Fe/Si
ggplot(data2, aes(x=AlFeSi, y=K2O, color=Phase)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("K"["2"] ~ "O"))
ggplot(data2, aes(x=AlFeSi, y=K2O, color=Level)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("K"["2"] ~ "O"))
ggplot(data2, aes(x=AlFeSi, y=K2O, color=Phase)) + geom_boxplot() + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("K"["2"] ~ "O"))
ggplot(data2, aes(x=AlFeSi, y=K2O, color=Level)) + geom_boxplot() + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("K"["2"] ~ "O"))
#CaO vs Al+Fe/Si
ggplot(data2, aes(x=AlFeSi, y=CaO, color=Phase)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("CaO"))
ggplot(data2, aes(x=AlFeSi, y=CaO, color=Level)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("CaO"))
ggplot(data2, aes(x=AlFeSi, y=CaO, color=Phase)) + geom_boxplot() + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("CaO"))
ggplot(data2, aes(x=AlFeSi, y=CaO, color=Level)) + geom_boxplot() + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("CaO"))
#TiO2 vs Al+Fe/Si
ggplot(data2, aes(x=AlFeSi, y=TiO2, color=Phase)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("Ti" ~ "O"["2"]))
ggplot(data2, aes(x=AlFeSi, y=TiO2, color=Level)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("Ti" ~ "O"["2"]))
ggplot(data2, aes(x=AlFeSi, y=TiO2, color=Phase)) + geom_boxplot() + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("Ti" ~ "O"["2"]))
ggplot(data2, aes(x=AlFeSi, y=TiO2, color=Level)) + geom_boxplot() + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("Ti" ~ "O"["2"]))
#MnO vs Al+Fe/Si
ggplot(data2, aes(x=AlFeSi, y=MnO, color=Phase)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("Mn" ~ "O"))
ggplot(data2, aes(x=AlFeSi, y=MnO, color=Level)) + geom_point(size=6) + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("Mn" ~ "O"))
ggplot(data2, aes(x=AlFeSi, y=MnO, color=Phase)) + geom_boxplot() + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("Mn" ~ "O"))
ggplot(data2, aes(x=AlFeSi, y=MnO, color=Level)) + geom_boxplot() + labs(x = expression("Al"["2"] ~ "O"["3"]~ "+ (Fe"["2"]~ "O"["3"]~ "/SiO"["2"]~ ")"))+ labs(y = expression("Mn" ~ "O"))
#bi-plots according to all major elements vs Si+Al
#Na2O vs Si+Al
ggplot(data2, aes(x=SiAl, y=Na2O, color=Phase)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+labs(y = expression("Na"["2"] ~ "O"))
ggplot(data2, aes(x=SiAl, y=Na2O, color=Level)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+labs(y = expression("Na"["2"] ~ "O"))
ggplot(data2, aes(x=SiAl, y=Na2O, color=Phase)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+labs(y = expression("Na"["2"] ~ "O"))
ggplot(data2, aes(x=SiAl, y=Na2O, color=Level)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+labs(y = expression("Na"["2"] ~ "O"))
#P2O5 vs Si+Al
ggplot(data2, aes(x=SiAl, y=P2O5, color=Phase)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("P"["2"] ~ "O"["5"]))
ggplot(data2, aes(x=SiAl, y=P2O5, color=Level)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("P"["2"] ~ "O"["5"]))
ggplot(data2, aes(x=SiAl, y=P2O5, color=Phase)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("P"["2"] ~ "O"["5"]))
ggplot(data2, aes(x=SiAl, y=P2O5, color=Level)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("P"["2"] ~ "O"["5"]))
#K2O vs Si+Al
ggplot(data2, aes(x=SiAl, y=K2O, color=Phase)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("K"["2"] ~ "O"))
ggplot(data2, aes(x=SiAl, y=K2O, color=Level)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("K"["2"] ~ "O"))
ggplot(data2, aes(x=SiAl, y=K2O, color=Phase)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("K"["2"] ~ "O"))
ggplot(data2, aes(x=SiAl, y=K2O, color=Level)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("K"["2"] ~ "O"))
#CaO vs Si+Al
ggplot(data2, aes(x=SiAl, y=CaO, color=Phase)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("CaO"))
ggplot(data2, aes(x=SiAl, y=CaO, color=Level)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("CaO"))
ggplot(data2, aes(x=SiAl, y=CaO, color=Phase)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("CaO"))
ggplot(data2, aes(x=SiAl, y=CaO, color=Level)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("CaO"))
#TiO2 vs Si+Al
ggplot(data2, aes(x=SiAl, y=TiO2, color=Phase)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("Ti" ~ "O"["2"]))
ggplot(data2, aes(x=SiAl, y=TiO2, color=Level)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("Ti" ~ "O"["2"]))
ggplot(data2, aes(x=SiAl, y=TiO2, color=Phase)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("Ti" ~ "O"["2"]))
ggplot(data2, aes(x=SiAl, y=TiO2, color=Level)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("Ti" ~ "O"["2"]))
#MnO vs Si+Al
ggplot(data2, aes(x=SiAl, y=MnO, color=Phase)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("Mn" ~ "O"))
ggplot(data2, aes(x=SiAl, y=MnO, color=Level)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("Mn" ~ "O"))
ggplot(data2, aes(x=SiAl, y=MnO, color=Phase)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("Mn" ~ "O"))
ggplot(data2, aes(x=SiAl, y=MnO, color=Level)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("Mn" ~ "O"))
#Mg+Mn+Fe vs Si+Al
ggplot(data2, aes(x=SiAl, y=MgMnFe, color=Phase)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("MgO"+"MnO"+"Fe"["2"]~ "O"["3"]))
ggplot(data2, aes(x=SiAl, y=MgMnFe, color=Level)) + geom_point(size=6) + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("MgO"+"MnO"+"Fe"["2"]~ "O"["3"]))
ggplot(data2, aes(x=SiAl, y=MgMnFe, color=Phase)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("MgO"+"MnO"+"Fe"["2"]~ "O"["3"]))
ggplot(data2, aes(x=SiAl, y=MgMnFe, color=Level)) + geom_boxplot() + labs(x = expression("Si O"["2"]~ "+ Al"["2"]~ "O"["3"]))+ labs(y = expression("MgO"+"MnO"+"Fe"["2"]~ "O"["3"]))
#Descriptives
library(tidyverse)
library(ggpubr)
library(rstatix)
level <- as.factor(data$Level)
phase<- as.factor(data$Phase)
summary(data)
#Calculation of the coefficient of variation
dataset <- data.frame(data$Na2O, data$MgO, data$Al2O3, data$SiO2, data$P2O5, data$K2O, data$CaO, data$TiO2, data$MnO, data$Fe2O3, stringsAsFactors = FALSE)
sapply(dataset, function(x) sd(x, na.rm=T) / mean(x, na.rm=T) * 100)
#KW Test
kruskal.test(data$Na2O ~ phase, data = data)
kruskal.test(data$MgO ~ phase, data = data)
kruskal.test(data$Al2O3 ~ phase, data = data)
kruskal.test(data$SiO2 ~ phase, data = data)
kruskal.test(data$P2O5 ~ phase, data = data)
kruskal.test(data$K2O ~ phase, data = data)
kruskal.test(data$CaO ~ phase, data = data)
kruskal.test(data$TiO2 ~ phase, data = data)
kruskal.test(data$MnO ~ phase, data = data)
kruskal.test(data$Fe2O3 ~ phase, data = data)
#MW (Wilcoxon rank-sum) Test
DATASET <- data.frame(data$Na2O, data$MgO, data$Al2O3, data$SiO2, data$P2O5, data$K2O, data$CaO, data$TiO2, data$MnO, data$Fe2O3, data$Level, stringsAsFactors = TRUE)
wilcox.test(data$Na2O ~ level, data = data, exact = FALSE)
wilcox.test(data$Al2O3 ~ level, data = data, exact = FALSE)
wilcox.test(data$SiO2 ~ level, data = data, exact = FALSE)
wilcox.test(data$P2O5 ~ level, data = data, exact = FALSE)
wilcox.test(data$K2O ~ level, data = data, exact = FALSE)
wilcox.test(data$CaO ~ level, data = data, exact = FALSE)
wilcox.test(data$TiO2 ~ level, data = data, exact = FALSE)
wilcox.test(data$MnO ~ level, data = data, exact = FALSE)
wilcox.test(data$Fe2O3 ~ level, data = data, exact = FALSE)
#PCA
install.packages("corrr")
library('corrr')
install.packages("ggcorrplot")
library(ggcorrplot)
install.packages("FactoMineR")
library("FactoMineR")
install.packages("devtools")
library("devtools")
install_github("kassambara/factoextra")
install.packages("factoextra")
library("factoextra")
numerical_data <- data[,4:13]
head(numerical_data)
corr_matrix <- cor(numerical_data)
ggcorrplot(corr_matrix)
data.pca <- princomp(corr_matrix)
summary(data.pca)
data.pca$loadings[, 1:2]
fviz_eig(data.pca, addlabels = TRUE)
# Graph of the variables
fviz_pca_var(data.pca, col.var = "black")
# Graph of the samples
res.pca <- prcomp(data[,4:13], scale = TRUE)
p <- fviz_pca_ind(res.pca, label="none", habillage=data$Phase,
addEllipses=TRUE, ellipse.level=0.95)
print(p)
fviz_pca_biplot(res.pca, label ="var")
#contribution of the variables
fviz_pca_var(res.pca, col.var="contrib")+
scale_color_gradient2(low="blue", mid="yellow",
high="red", midpoint=96) +
theme_minimal()
#Cluster
#Step 1 : Scale all variables to have mean = 0 and standard deviation = 1
clusterdata <- dataset %>% mutate_all(~(scale(.) %>% as.vector))
#Step 2 : Calculating Euclidean Distances
dist_mat <- dist(clusterdata, method = 'euclidean')
#Step 3 : Clustering w/ Average-linkage method
hclust_avg <- hclust(dist_mat, method = 'average')
plot(hclust_avg)
rect.hclust(hclust_avg , k = 3, border = 2:6)
abline(h = 3, col = 'red')
suppressPackageStartupMessages(library(dendextend))
avg_dend_obj <- as.dendrogram(hclust_avg)
avg_col_dend <- color_branches(avg_dend_obj, h = 3)
plot(avg_col_dend)