-
Notifications
You must be signed in to change notification settings - Fork 2
/
R_Homework_Carley.Rmd
355 lines (311 loc) · 13.7 KB
/
R_Homework_Carley.Rmd
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
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
---
title: "R_Homework"
author: "ClayBae"
date: "10/17/2019"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Load Libraries
```{r}
if (!require("tidyverse")) install.packages("tidyverse")
library(tidyverse)
if (!require("ggplot2")) install.packages("ggplot2")
library(ggplot2)
if (!require("gtools")) install.packages("gtools")
library(gtools)
if (!require("reshape2")) install.packages("reshape2")
library(reshape2)
if (!require("httr")) install.packages("httr")
library(httr)
```
#Import Data
```{r}
SNP <- read_tsv("https://raw.githubusercontent.com/EEOB-BioData/BCB546X-Fall2019/master/assignments/UNIX_Assignment/snp_position.txt")
Fang <- read_tsv("https://raw.githubusercontent.com/EEOB-BioData/BCB546X-Fall2019/master/assignments/UNIX_Assignment/fang_et_al_genotypes.txt")
```
# Data Inspection
```{r}
view(SNP)
str(SNP)
view(Fang)
str(Fang)
```
# Make files for future outputs
```{r}
dir.create("Maize")
dir.create("Teosinte")
dir.create("graphs")
```
## Data Processing
```{r}
ShortSNP <- SNP[ ,c(1,3,4)] ##makes new tibble of SNP_ID, Chromosome, and Position
```
# Process Full Dataset
```{r}
transposedFang <- as.data.frame(t(Fang))
names(transposedFang) <- lapply(transposedFang[1, ], as.character) #Make the sample names the col names
transposedFang <- transposedFang[-1,] #Remove sample names row
transposedFang <- rownames_to_column(transposedFang, var="SNP_ID") #Makes a col of the row names
mergedFangSNP <- merge(ShortSNP,transposedFang, by.x="SNP_ID", by.y="SNP_ID", all = TRUE)
```
## Pull Species
Since 'group' isn't included in the merge each species has to be pulled out first then merged.
# Maize
Maize = ZMMIL, ZMMLR, and ZMMMR
```{r}
maize <- filter(Fang, Group == "ZMMIL" | Group == "ZMMLR" | Group == "ZMMMR")
maize_names <- maize[,c(1:3)]
maize_names$full <- apply(maize_names, 1, paste, collapse = ", ") #Makes a new col of the full name
```
# Teosinte
Teosinte = ZMPBA, ZMPIL, and ZMPJA
```{r}
teosinte <- filter(Fang, Group == "ZMPBA" | Group == "ZMPIL" | Group == "ZMPJA")
teosinte_names <- teosinte[,c(1:3)]
teosinte_names$full <- apply(teosinte_names, 1, paste, collapse = ", ") #Makes a new col of the full name
```
# Transpose maize files
```{r}
tmaize <- as.data.frame(t(maize[,c(-1:-3)]))
colnames(tmaize) <- maize_names$full
rnames <- as.data.frame(rownames(tmaize))
rownames(tmaize) <- NULL
tmaize <- cbind(rnames,tmaize)
colnames(tmaize)[1] <- "SNP_ID"
```
# Join SNP and maizeFang
```{r}
mergedmaize <- inner_join(x = ShortSNP, y = tmaize, by = "SNP_ID")
```
# Transpose teosinte files
```{r}
tteosinte <- as.data.frame(t(teosinte[,c(-1:-3)]))
colnames(tteosinte) <- teosinte_names$full
rnames <- as.data.frame(rownames(tteosinte))
rownames(tteosinte) <- NULL
tteosinte <- cbind(rnames,tteosinte)
colnames(tteosinte)[1] <- "SNP_ID"
```
# Join SNP and teosinteFang
```{r}
mteosinte <- inner_join(x = ShortSNP, y = tteosinte, by = "SNP_ID")
```
## Creating Files for miaze then teosinte
# Sort Maize by increasing 'Position'
```{r}
mergedmaize <- mergedmaize[mixedorder(mergedmaize$Position),]
```
# Create new files for each 'Chromosome'
```{r}
maize_chrom01_increase <- filter(mergedmaize, Chromosome == "1") %>% write_csv(path = "Maize/maize_chrom01_increase.csv")
maize_chrom02_increase <- filter(mergedmaize, Chromosome == "2") %>% write_csv(path = "Maize/maize_chrom02_increase.csv")
maize_chrom03_increase <- filter(mergedmaize, Chromosome == "3") %>% write_csv(path = "Maize/maize_chrom03_increase.csv")
maize_chrom04_increase <- filter(mergedmaize, Chromosome == "4") %>% write_csv(path = "Maize/maize_chrom04_increase.csv")
maize_chrom05_increase <- filter(mergedmaize, Chromosome == "5") %>% write_csv(path = "Maize/maize_chrom05_increase.csv")
maize_chrom06_increase <- filter(mergedmaize, Chromosome == "6") %>% write_csv(path = "Maize/maize_chrom06_increase.csv")
maize_chrom07_increase <- filter(mergedmaize, Chromosome == "7") %>% write_csv(path = "Maize/maize_chrom07_increase.csv")
maize_chrom08_increase <- filter(mergedmaize, Chromosome == "8") %>% write_csv(path = "Maize/maize_chrom08_increase.csv")
maize_chrom09_increase <- filter(mergedmaize, Chromosome == "9") %>% write_csv(path = "Maize/maize_chrom09_increase.csv")
maize_chrom10_increase <- filter(mergedmaize, Chromosome == "10") %>% write_csv(path = "Maize/maize_chrom10_increase.csv")
```
# Sort Maize by decreasing 'Position'
```{r}
mergedmaize <- mergedmaize[mixedorder(mergedmaize$Position, decreasing = T),]
```
# Replace ?/? with -/-
```{r}
mergedmaize <- apply(X = mergedmaize, MARGIN = 2, FUN = as.character)
mergedmaize[mergedmaize == "?/?"] <- "-/-"
mergedmaize <- as.data.frame(mergedmaize)
```
# Create new files for each 'Chromosome'
```{r}
maize_chrom01_decrease <- filter(mergedmaize, Chromosome == "1") %>% write_csv(path = "Maize/maize_chrom01_decrease_changed_missing_data.csv")
maize_chrom02_decrease <- filter(mergedmaize, Chromosome == "2") %>% write_csv(path = "Maize/maize_chrom02_decrease_changed_missing_data.csv")
maize_chrom03_decrease <- filter(mergedmaize, Chromosome == "3") %>% write_csv(path = "Maize/maize_chrom03_decrease_changed_missing_data.csv")
maize_chrom04_decrease <- filter(mergedmaize, Chromosome == "4") %>% write_csv(path = "Maize/maize_chrom04_decrease_changed_missing_data.csv")
maize_chrom05_decrease <- filter(mergedmaize, Chromosome == "5") %>% write_csv(path = "Maize/maize_chrom05_decrease_changed_missing_data.csv")
maize_chrom06_decrease <- filter(mergedmaize, Chromosome == "6") %>% write_csv(path = "Maize/maize_chrom06_decrease_changed_missing_data.csv")
maize_chrom07_decrease <- filter(mergedmaize, Chromosome == "7") %>% write_csv(path = "Maize/maize_chrom07_decrease_changed_missing_data.csv")
maize_chrom08_decrease <- filter(mergedmaize, Chromosome == "8") %>% write_csv(path = "Maize/maize_chrom08_decrease_changed_missing_data.csv")
maize_chrom09_decrease <- filter(mergedmaize, Chromosome == "9") %>% write_csv(path = "Maize/maize_chrom09_decrease_changed_missing_data.csv")
maize_chrom10_decrease <- filter(mergedmaize, Chromosome == "10") %>% write_csv(path = "Maize/maize_chrom10_decrease_changed_missing_data.csv")
```
# Sort teosinte by increasing 'Position'
```{r}
mteosinte <- mteosinte[mixedorder(mteosinte$Position),]
```
# Create new files for each 'Chromosome'
```{r}
teosinte_chrom01_increase <- filter(mteosinte, Chromosome == "1") %>% write_csv(path = "Teosinte/teosinte_chrom01_increase.csv")
teosinte_chrom02_increase <- filter(mteosinte, Chromosome == "2") %>% write_csv(path = "Teosinte/teosinte_chrom02_increase.csv")
teosinte_chrom03_increase <- filter(mteosinte, Chromosome == "3") %>% write_csv(path = "Teosinte/teosinte_chrom03_increase.csv")
teosinte_chrom04_increase <- filter(mteosinte, Chromosome == "4") %>% write_csv(path = "Teosinte/teosinte_chrom04_increase.csv")
teosinte_chrom05_increase <- filter(mteosinte, Chromosome == "5") %>% write_csv(path = "Teosinte/teosinte_chrom05_increase.csv")
teosinte_chrom06_increase <- filter(mteosinte, Chromosome == "6") %>% write_csv(path = "Teosinte/teosinte_chrom06_increase.csv")
teosinte_chrom07_increase <- filter(mteosinte, Chromosome == "7") %>% write_csv(path = "Teosinte/teosinte_chrom07_increase.csv")
teosinte_chrom08_increase <- filter(mteosinte, Chromosome == "8") %>% write_csv(path = "Teosinte/teosinte_chrom08_increase.csv")
teosinte_chrom09_increase <- filter(mteosinte, Chromosome == "9") %>% write_csv(path = "Teosinte/teosinte_chrom09_increase.csv")
teosinte_chrom10_increase <- filter(mteosinte, Chromosome == "10") %>% write_csv(path = "Teosinte/teosinte_chrom10_increase.csv")
```
# Sort teosinte by decreasing 'Position'
```{r}
mteosinte <- mteosinte[mixedorder(mteosinte$Position, decreasing = T),]
```
# Replace ?/? with -/-
```{r}
mteosinte <- apply(X = mteosinte, MARGIN = 2, FUN = as.character)
mteosinte[mteosinte == "?/?"] <- "-/-"
mteosinte <- as.data.frame(mteosinte)
```
# Create new files for each 'Chromosome'
```{r}
teosinte_chrom01_decrease <- filter(mteosinte, Chromosome == "1") %>% write_csv(path = "Teosinte/teosinte_chrom01_decrease_changed_missing_data.csv")
teosinte_chrom02_decrease <- filter(mteosinte, Chromosome == "2") %>% write_csv(path = "Teosinte/teosinte_chrom02_decrease_changed_missing_data.csv")
teosinte_chrom03_decrease <- filter(mteosinte, Chromosome == "3") %>% write_csv(path = "Teosinte/teosinte_chrom03_decrease_changed_missing_data.csv")
teosinte_chrom04_decrease <- filter(mteosinte, Chromosome == "4") %>% write_csv(path = "Teosinte/teosinte_chrom04_decrease_changed_missing_data.csv")
teosinte_chrom05_decrease <- filter(mteosinte, Chromosome == "5") %>% write_csv(path = "Teosinte/teosinte_chrom05_decrease_changed_missing_data.csv")
teosinte_chrom06_decrease <- filter(mteosinte, Chromosome == "6") %>% write_csv(path = "Teosinte/teosinte_chrom06_decrease_changed_missing_data.csv")
teosinte_chrom07_decrease <- filter(mteosinte, Chromosome == "7") %>% write_csv(path = "Teosinte/teosinte_chrom07_decrease_changed_missing_data.csv")
teosinte_chrom08_decrease <- filter(mteosinte, Chromosome == "8") %>% write_csv(path = "Teosinte/teosinte_chrom08_decrease_changed_missing_data.csv")
teosinte_chrom09_decrease <- filter(mteosinte, Chromosome == "9") %>% write_csv(path = "Teosinte/teosinte_chrom09_decrease_changed_missing_data.csv")
teosinte_chrom10_decrease <- filter(mteosinte, Chromosome == "10") %>% write_csv(path = "Teosinte/teosinte_chrom10_decrease_changed_missing_data.csv")
```
## homozygous vs. heterozygous
#Melt the original Fang file
```{r}
zygo_long <- filter(Fang, Group == "ZMMIL" | Group == "ZMMLR" | Group == "ZMMMR" | Group == "ZMPBA" | Group == "ZMPIL" | Group == "ZMPJA")
zygo <- melt(zygo_long, measure.vars = colnames(Fang)[4:986])
colnames(zygo)[4:5] <- c("SNP_ID", "Homozygous")
colnames(zygo)
```
#Change all homozygous SNPs to TRUE
```{r}
zygo[zygo == "A/A"] <- TRUE
zygo[zygo == "C/C"] <- TRUE
zygo[zygo == "G/G"] <- TRUE
zygo[zygo == "T/T"] <- TRUE
```
#Change all heterozygo to FALSE
```{r}
zygo[zygo == "A/C"] <- FALSE
zygo[zygo == "A/G"] <- FALSE
zygo[zygo == "A/T"] <- FALSE
zygo[zygo == "C/G"] <- FALSE
zygo[zygo == "C/T"] <- FALSE
zygo[zygo == "G/T"] <- FALSE
```
#Change all missing values to NA
```{r}
zygo[zygo == "?/?"] <- NA
```
#Sort the dataframe using "Group" and "Species_ID"
```{r}
zygo <- arrange(zygo, Sample_ID, Group)
```
## Data Visualization
# SNPs per chromosome
```{r}
ggplot(data = mergedFangSNP) +
geom_bar(mapping = aes(x = Chromosome)) +
scale_x_discrete(limits=c(1:10, "unknown", "multiple")) +
ggtitle(label = "SNPs per chromosome") +
xlab(label = "Chromosome") +
ylab(label = "Number of SNPs") +
theme(
plot.title = element_text(hjust = 0.5, size = 20),
axis.text = element_text(size = 15),
axis.title = element_text(size = 15)
)
ggsave(filename = "graphs/SNPs per chromosome.png", device = "png")
```
# Missing data and amout of heterozygosity
```{r}
ggplot(data = zygo) +
geom_bar(mapping = aes(x = Homozygous, fill = Homozygous), stat = "count") +
ggtitle(label = "Total SNP Zygosity") +
ylab(label = "Number of SNPs") +
theme(
plot.title = element_text(hjust = 0.5, size = 15),
axis.text = element_text(size = 12),
axis.title = element_text(size = 12),
legend.position = "none"
)
ggsave(filename = "graphs/Total SNP Zygosity.png", device = "png")
```
# SNPs per Group
```{r}
ggplot(data = Fang) +
geom_bar(mapping = aes(x = Group)) +
ggtitle(label = "SNPs per Group") +
ylab("Number of SNPs") +
theme(
plot.title = element_text(hjust = 0.5, size = 15),
axis.text = element_text(size = 9),
axis.title = element_text(size = 12)
)
ggsave(filename = "graphs/SNPs per Group.png", device = "png")
```
# SNP Zygosity by Sample_ID
```{r}
ggplot(data = zygo) +
geom_bar(mapping = aes(x = Sample_ID, fill = Homozygous), stat = "count") +
ggtitle(label = "SNP Zygosity by Ordered Sample_ID") +
ylab(label = "Number of SNPs") +
theme(
plot.title = element_text(hjust = 0.5),
axis.text.x = element_blank(),
axis.ticks.x = element_blank()
)
ggsave(filename = "graphs/SNP Zygosity by Ordered Sample_ID.png", device = "png")
```
# SNP Zygosity by Group
```{r}
ggplot(data = zygo) +
geom_bar(mapping = aes(x = Group, fill = Homozygous), stat = "count") +
ggtitle(label = "SNP Zygosity by Group") +
xlab(label = "Chromosome") +
ylab(label = "Number of SNPs") +
theme(
plot.title = element_text(hjust = 0.5, size = 15),
axis.text = element_text(size = 12),
axis.title = element_text(size = 12)
)
ggsave(filename = "graphs/SNP Zygosity by Group.png", device = "png")
```
# Position Adjustment for SNP Zygosity by Group
```{r}
ggplot(data = zygo) +
geom_bar(mapping = aes(x = Group, fill = Homozygous), position = "fill") +
ggtitle(label = "Position Adjustment for SNP Zygosity by Group") +
xlab(label = "Chromosome") +
ylab(label = "Number of SNPs") +
theme(
plot.title = element_text(hjust = 0.5, size = 15),
axis.text = element_text(size = 12),
axis.title = element_text(size = 12)
)
ggsave(filename = "graphs/Position Adjustment for SNP Zygosity by Group.png", device = "png")
```
## Additional visualization
# Distribution of SNPs across chromosomes
```{r}
df <- mergedFangSNP %>%
mutate(Dist_Bin = cut(as.numeric(Position), breaks = 20))
df1 <- subset(df, Chromosome != "unknown")
df2 <- subset(df1, Chromosome != "NA")
df3 <- subset(df2, Chromosome != "multiple")
ggplot(data = df3) +
theme(
plot.title = element_text(hjust = 0.5),
axis.text.x = element_text(angle = 315, hjust = -0.02, size = 5)
) +
facet_wrap(~Chromosome, scales = "free", nrow = 2) +
geom_bar(mapping = aes(x = Dist_Bin), stat = "count") +
ggtitle(label = "Distribution of SNPs across chromosomes") +
xlab(label = "Position Binned") +
ylab(label = "Number of SNPs")
ggsave(filename = "graphs/Distribution of SNPs across chromosomes.png", device = "png")
```