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Update Allstats.R
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‎R/Allstats.R

+43-38
Original file line numberDiff line numberDiff line change
@@ -13,16 +13,21 @@
1313
#'
1414
Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
1515
{
16+
1617
LETTERS702 <- c(sapply(LETTERS, function(x) paste0(x, LETTERS)))
1718
LETTERS37232 <- c(LETTERS, LETTERS702, sapply(LETTERS, function(x) paste0(x,
1819
LETTERS702)))
19-
LETTERS37232 <- LETTERS37232[-365]
20+
LETTERS210729 <- c(LETTERS, LETTERS702,LETTERS37232, sapply(LETTERS, function(x) paste0(x,
21+
LETTERS37232)))
22+
LETTERS210729 <- LETTERS210729[-365]
23+
LETTERS210729<-LETTERS210729[-10205]
24+
LETTERS210729<-LETTERS210729[-267101]
2025
colnames(Data) <- Data[1, ]
2126
Data <- Data[-1, -2]
2227
Data<-Data %>% dplyr::arrange(Group)
2328
Data_renamed <- Data
2429
nmet <- ncol(Data) - 2
25-
colnames(Data_renamed) <- c(colnames(Data[1:2]), LETTERS37232[1:nmet])
30+
colnames(Data_renamed) <- c(colnames(Data[1:2]), LETTERS210729[1:nmet])
2631
rownames(Data_renamed) <- Data[, 1]
2732
Data_renamed_raw <- Data_renamed[, -c(1, 2)]
2833
Data_renamed_raw <- apply(Data_renamed_raw, 2, as.numeric)
@@ -45,14 +50,14 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
4550
}
4651
else {
4752
for (met in 1:(ncol(Data) - 2)) {
48-
assign(paste(as.character(LETTERS37232[met]),
53+
assign(paste(as.character(LETTERS210729[met]),
4954
unique(Data$Group)[Gnum_1], unique(Data$Group)[Gnum_2],
5055
"T_test", sep = "_"), t.test(x = (eval(parse(text = paste("Data",
5156
unique(Data$Group)[Gnum_1], sep = "_")))[,
52-
eval(parse(text = "LETTERS37232[met]"))]),
57+
eval(parse(text = "LETTERS210729[met]"))]),
5358
y = (eval(parse(text = paste("Data",
5459
unique(Data$Group)[Gnum_2], sep = "_")))[,
55-
eval(parse(text = "LETTERS37232[met]"))]))[["p.value"]])
60+
eval(parse(text = "LETTERS210729[met]"))]))[["p.value"]])
5661
}
5762
}
5863
}
@@ -65,7 +70,7 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
6570
else {
6671
if (is.na(Result[1, Rounder]) == T) {
6772
for (met_1 in 1:(ncol(Data_final) - 2)) {
68-
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
73+
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
6974
unique(Data$Group)[C], unique(Data$Group)[H],
7075
"T_test", sep = "_")))
7176
}
@@ -82,14 +87,14 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
8287
}
8388
else {
8489
for (met in 1:(ncol(Data) - 2)) {
85-
assign(paste(as.character(LETTERS37232[met]),
90+
assign(paste(as.character(LETTERS210729[met]),
8691
unique(Data$Group)[Gnum_1], unique(Data$Group)[Gnum_2],
8792
"U_test", sep = "_"), wilcox.test(x = (eval(parse(text = paste("Data",
8893
unique(Data$Group)[Gnum_1], sep = "_")))[,
89-
eval(parse(text = "LETTERS37232[met]"))]),
94+
eval(parse(text = "LETTERS210729[met]"))]),
9095
y = (eval(parse(text = paste("Data",
9196
unique(Data$Group)[Gnum_2], sep = "_")))[,
92-
eval(parse(text = "LETTERS37232[met]"))]))[["p.value"]])
97+
eval(parse(text = "LETTERS210729[met]"))]))[["p.value"]])
9398
}
9499
}
95100
}
@@ -102,7 +107,7 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
102107
else {
103108
if (is.na(Result[1, Rounder]) == T) {
104109
for (met_1 in 1:(ncol(Data_final) - 2)) {
105-
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
110+
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
106111
unique(Data$Group)[C], unique(Data$Group)[H],
107112
"U_test", sep = "_")))
108113
}
@@ -143,7 +148,7 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
143148
print("###########################################")
144149
}
145150
rm(list = setdiff(ls(), c("Data_renamed", "Data",
146-
"Result", "LETTERS37232", "event",
151+
"Result", "LETTERS210729", "event",
147152
"P_hoc", "Colors", "significant_variable_only")))
148153
print("statistical test has finished")
149154
Result_T <- Result[, 1]
@@ -176,14 +181,14 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
176181
}
177182
else {
178183
for (met in 1:(ncol(Data) - 2)) {
179-
assign(paste(as.character(LETTERS37232[met]),
184+
assign(paste(as.character(LETTERS210729[met]),
180185
unique(Data$Group)[Gnum_1], unique(Data$Group)[Gnum_2],
181186
"T_test", sep = "_"), t.test(x = (eval(parse(text = paste("Data",
182187
unique(Data$Group)[Gnum_1], sep = "_")))[,
183-
eval(parse(text = "LETTERS37232[met]"))]),
188+
eval(parse(text = "LETTERS210729[met]"))]),
184189
y = (eval(parse(text = paste("Data",
185190
unique(Data$Group)[Gnum_2], sep = "_")))[,
186-
eval(parse(text = "LETTERS37232[met]"))]))[["p.value"]])
191+
eval(parse(text = "LETTERS210729[met]"))]))[["p.value"]])
187192
}
188193
}
189194
}
@@ -196,7 +201,7 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
196201
else {
197202
if (is.na(Result[1, Rounder]) == T) {
198203
for (met_1 in 1:(ncol(Data_final) - 2)) {
199-
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
204+
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
200205
unique(Data$Group)[C], unique(Data$Group)[H],
201206
"T_test", sep = "_")))
202207
}
@@ -213,14 +218,14 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
213218
}
214219
else {
215220
for (met in 1:(ncol(Data) - 2)) {
216-
assign(paste(as.character(LETTERS37232[met]),
221+
assign(paste(as.character(LETTERS210729[met]),
217222
unique(Data$Group)[Gnum_1], unique(Data$Group)[Gnum_2],
218223
"U_test", sep = "_"), wilcox.test(x = (eval(parse(text = paste("Data",
219224
unique(Data$Group)[Gnum_1], sep = "_")))[,
220-
eval(parse(text = "LETTERS37232[met]"))]),
225+
eval(parse(text = "LETTERS210729[met]"))]),
221226
y = (eval(parse(text = paste("Data",
222227
unique(Data$Group)[Gnum_2], sep = "_")))[,
223-
eval(parse(text = "LETTERS37232[met]"))]))[["p.value"]])
228+
eval(parse(text = "LETTERS210729[met]"))]))[["p.value"]])
224229
}
225230
}
226231
}
@@ -233,7 +238,7 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
233238
else {
234239
if (is.na(Result[1, Rounder]) == T) {
235240
for (met_1 in 1:(ncol(Data_final) - 2)) {
236-
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
241+
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
237242
unique(Data$Group)[C], unique(Data$Group)[H],
238243
"U_test", sep = "_")))
239244
}
@@ -244,14 +249,14 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
244249
}
245250
print("U-test has finished")
246251
for (met in 1:(ncol(Data) - 2)) {
247-
Ano_In <- aov(eval(parse(text = LETTERS37232[met])) ~
252+
Ano_In <- aov(eval(parse(text = LETTERS210729[met])) ~
248253
Group, data = Data_final)
249-
assign(paste(as.character(LETTERS37232[met]),
254+
assign(paste(as.character(LETTERS210729[met]),
250255
"Anova", sep = "_"), summary(Ano_In)[[1]][["Pr(>F)"]][1])
251256
}
252257
if (is.na(Result[1, Rounder]) == T) {
253258
for (met_1 in 1:(ncol(Data_final) - 2)) {
254-
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
259+
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
255260
"Anova", sep = "_")))
256261
}
257262
Rounder <- Rounder + 1
@@ -260,15 +265,15 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
260265
print("Anova went wrong")
261266
}
262267
for (met in 1:(ncol(Data) - 2)) {
263-
assign(paste(LETTERS37232[met], "Anova_Post_Hoc",
264-
sep = "_"), DescTools::PostHocTest(aov(eval(parse(text = LETTERS37232[met])) ~
268+
assign(paste(LETTERS210729[met], "Anova_Post_Hoc",
269+
sep = "_"), DescTools::PostHocTest(aov(eval(parse(text = LETTERS210729[met])) ~
265270
Group, data = Data_final), method = "scheffe"))
266271
}
267-
for (Ano_numb in 1:nrow(eval(parse(text = paste(LETTERS37232[met],
272+
for (Ano_numb in 1:nrow(eval(parse(text = paste(LETTERS210729[met],
268273
"Anova_Post_Hoc", sep = "_")))[["Group"]])) {
269274
if (is.na(Result[1, Rounder]) == T) {
270275
for (met_1 in 1:(ncol(Data_final) - 2)) {
271-
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
276+
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
272277
"Anova_Post_Hoc", sep = "_")))[["Group"]][Ano_numb,
273278
4]
274279
}
@@ -280,14 +285,14 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
280285
}
281286
print("Anova & PostHoc has finished")
282287
for (met in 1:(ncol(Data) - 2)) {
283-
Kru_In <- kruskal.test(eval(parse(text = LETTERS37232[met])) ~
288+
Kru_In <- kruskal.test(eval(parse(text = LETTERS210729[met])) ~
284289
Group, data = Data_final)
285-
assign(paste(as.character(LETTERS37232[met]),
290+
assign(paste(as.character(LETTERS210729[met]),
286291
"Kruskal_Wallis", sep = "_"), Kru_In[["p.value"]])
287292
}
288293
if (is.na(Result[1, Rounder]) == T) {
289294
for (met_1 in 1:(ncol(Data_final) - 2)) {
290-
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
295+
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
291296
"Kruskal_Wallis", sep = "_")))
292297
}
293298
Rounder <- Rounder + 1
@@ -296,15 +301,15 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
296301
print("Kruskal went wrong")
297302
}
298303
for (met in 1:(ncol(Data) - 2)) {
299-
assign(paste(LETTERS37232[met], "Dunn_Post_Hoc",
300-
sep = "_"), FSA::dunnTest(eval(parse(text = LETTERS37232[met])) ~
304+
assign(paste(LETTERS210729[met], "Dunn_Post_Hoc",
305+
sep = "_"), FSA::dunnTest(eval(parse(text = LETTERS210729[met])) ~
301306
Group, data = Data_final, method = "bh"))
302307
}
303-
for (Kru_numb in 1:length(eval(parse(text = paste(LETTERS37232[met],
308+
for (Kru_numb in 1:length(eval(parse(text = paste(LETTERS210729[met],
304309
"Dunn_Post_Hoc", sep = "_")))[["res"]][["Comparison"]])) {
305310
if (is.na(Result[1, Rounder]) == T) {
306311
for (met_1 in 1:(ncol(Data_final) - 2)) {
307-
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
312+
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
308313
"Dunn_Post_Hoc", sep = "_")))[["res"]][["P.adj"]][Kru_numb]
309314
}
310315
Rounder <- Rounder + 1
@@ -327,15 +332,15 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
327332
}
328333
}
329334
AN_Post_names <- NULL
330-
for (nrow in 1:nrow(eval(parse(text = paste(LETTERS37232[met],
335+
for (nrow in 1:nrow(eval(parse(text = paste(LETTERS210729[met],
331336
"Anova_Post_Hoc", sep = "_")))[["Group"]])) {
332-
AN_Post_names <- rbind(AN_Post_names, rownames(eval(parse(text = paste(LETTERS37232[met],
337+
AN_Post_names <- rbind(AN_Post_names, rownames(eval(parse(text = paste(LETTERS210729[met],
333338
"Anova_Post_Hoc", sep = "_")))[["Group"]])[nrow])
334339
}
335340
DU_post_names <- NULL
336-
for (nrow in 1:length(eval(parse(text = paste(LETTERS37232[met],
341+
for (nrow in 1:length(eval(parse(text = paste(LETTERS210729[met],
337342
"Dunn_Post_Hoc", sep = "_")))[["res"]][["Comparison"]])) {
338-
DU_post_names <- rbind(DU_post_names, (eval(parse(text = paste(LETTERS37232[met],
343+
DU_post_names <- rbind(DU_post_names, (eval(parse(text = paste(LETTERS210729[met],
339344
"Dunn_Post_Hoc", sep = "_")))[["res"]][["Comparison"]])[nrow])
340345
}
341346
rownames(Result) <- colnames(Data)[3:(ncol(Data_final))]
@@ -360,7 +365,7 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
360365
print("###########################################")
361366
}
362367
rm(list = setdiff(ls(), c("Data_renamed", "Data",
363-
"Result", "LETTERS37232", "event",
368+
"Result", "LETTERS210729", "event",
364369
"P_hoc", "Colors", "significant_variable_only")))
365370
print("statistical test has finished")
366371
})

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