-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathbedtools_missing_display.R
163 lines (117 loc) · 6.44 KB
/
bedtools_missing_display.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
library(csv)
library(dplyr)
library(ggplot2)
library(RColorBrewer)
library(ggsci)
library(tidyr)
######################################
#getting the data
path = toString(commandArgs(TRUE)[1])
path_data_A = toString(commandArgs(TRUE)[2])
path_data_B = toString(commandArgs(TRUE)[3])
symbol_A = toString(commandArgs(TRUE)[4])
symbol_B = toString(commandArgs(TRUE)[5])
path = paste(path,symbol_A,"VS",symbol_B,"/", sep = "")
path_missing_A = paste(path,symbol_A,"_absent_in_",symbol_B,".csv", sep = "")
path_missing_B = paste(path,symbol_B,"_absent_in_",symbol_A,".csv", sep = "")
path_res = path
missing_A = read.csv(path_missing_A,header = TRUE, sep = "\t")
missing_B = read.csv(path_missing_B,header = TRUE, sep = "\t")
total_A = read.csv(path_data_A, header = TRUE, sep = "\t")
total_B = read.csv(path_data_B, header = TRUE, sep = "\t")
#######################################
#shaping the data which doesn't match
missing_A = separate(missing_A,col = repeat_class_family,sep = '/',into = c('repeat_class','repeat_family'))
missing_B = separate(missing_B,col = repeat_class_family,sep = '/',into = c('repeat_class','repeat_family'))
missing_A$repeat_class = gsub("?",'',missing_A$repeat_class, fixed = TRUE)
missing_A$repeat_class = gsub('Unspecified','Unknown',missing_A$repeat_class, fixed = TRUE)
missing_A$repeat_class = gsub('snRNA|tRNA|scRNA|rRNA','snRNA/tRNA/scRNA/rRNA',missing_A$repeat_class)
missing_B$repeat_class = gsub("?",'',missing_B$repeat_class, fixed = TRUE)
missing_B$repeat_class = gsub('Unspecified','Unknown',missing_B$repeat_class, fixed = TRUE)
missing_B$repeat_class = gsub('snRNA|tRNA|scRNA|rRNA','snRNA/tRNA/scRNA/rRNA',missing_B$repeat_class)
#######################################
#shaping the total data
total_A = separate(total_A,col = repeat_class_family,sep = '/',into = c('repeat_class','repeat_family'))
total_B = separate(total_B,col = repeat_class_family,sep = '/',into = c('repeat_class','repeat_family'))
total_A$repeat_class = gsub("?",'',total_A$repeat_class, fixed = TRUE)
total_A$repeat_class = gsub('Unspecified','Unknown',total_A$repeat_class, fixed = TRUE)
total_A$repeat_class = gsub('snRNA|tRNA|scRNA|rRNA','snRNA/tRNA/scRNA/rRNA',total_A$repeat_class)
total_B$repeat_class = gsub("?",'',total_B$repeat_class, fixed = TRUE)
total_B$repeat_class = gsub('Unspecified','Unknown',total_B$repeat_class, fixed = TRUE)
total_B$repeat_class = gsub('snRNA|tRNA|scRNA|rRNA','snRNA/tRNA/scRNA/rRNA',total_B$repeat_class)
#######################################
#counting the missing data by class
missing_A_class_count = missing_A %>% count(repeat_class)
missing_B_class_count = missing_B %>% count(repeat_class)
total_A_class_count = total_A %>% count(repeat_class)
total_B_class_count = total_B %>% count(repeat_class)
######################################
#barplots of the missing data by class for A
a = ggplot(missing_A_class_count, aes(x=repeat_class, fill=repeat_class, y=n)) +
geom_bar(stat = "identity") +
scale_fill_brewer(palette="Paired")+
theme(axis.text.x = element_text(angle = 25, hjust = 1))+
ggsave(paste(path_res,symbol_A,'missing.png', sep = ""), height = 5, width =10)
b = ggplot(missing_A_class_count, aes(x=repeat_class, fill=repeat_class, y=n)) +
geom_bar(stat = "identity") +
scale_y_log10()+
scale_fill_brewer(palette="Paired")+
theme(axis.text.x = element_text(angle = 25, hjust = 1))+
ggsave(paste(path_res,symbol_A,'missing_log.png', sep = ""), height = 5, width =10)
#barplots of the missing data by class for B
c = ggplot(missing_B_class_count, aes(x=repeat_class, fill=repeat_class, y=n)) +
geom_bar(stat = "identity") +
scale_fill_brewer(palette="Paired")+
theme(axis.text.x = element_text(angle = 25, hjust = 1))+
ggsave(paste(path_res,symbol_B,'missing.png', sep = ""), height = 5, width =10)
d = ggplot(missing_B_class_count, aes(x=repeat_class, fill=repeat_class, y=n)) +
geom_bar(stat = "identity") +
scale_fill_brewer(palette="Paired")+
scale_y_log10()+
theme(axis.text.x = element_text(angle = 25, hjust = 1))+
ggsave(paste(path_res,symbol_B,'missing_log.png', sep = ""), height = 5, width =10)
####################################
# barplot of the total data for A
e = ggplot(total_A_class_count, aes(x=repeat_class, fill=repeat_class, y=n)) +
geom_bar(stat = "identity") +
scale_fill_brewer(palette="Paired")+
theme(axis.text.x = element_text(angle = 25, hjust = 1))+
ggsave(paste(path_res,symbol_A,'total.png', sep = ""), height = 5, width =10)
f = ggplot(total_A_class_count, aes(x=repeat_class, fill=repeat_class, y=n)) +
geom_bar(stat = "identity") +
scale_y_log10()+
scale_fill_brewer(palette="Paired")+
theme(axis.text.x = element_text(angle = 25, hjust = 1))+
ggsave(paste(path_res,symbol_A,'total_log.png', sep = ""), height = 5, width =10)
#barplot of the total data for B
g = ggplot(total_B_class_count, aes(x=repeat_class, fill=repeat_class, y=n)) +
geom_bar(stat = "identity") +
scale_fill_brewer(palette="Paired")+
theme(axis.text.x = element_text(angle = 25, hjust = 1))+
ggsave(paste(path_res,symbol_B,'total.png', sep = ""), height = 5, width =10)
h = ggplot(total_B_class_count, aes(x=repeat_class, fill=repeat_class, y=n)) +
geom_bar(stat = "identity") +
scale_y_log10()+
scale_fill_brewer(palette="Paired")+
theme(axis.text.x = element_text(angle = 25, hjust = 1))+
ggsave(paste(path_res,symbol_B,'total_log.png', sep = ""), height = 5, width =10)
##############################################
#percent of unmatched data for A and B :
colnames(total_A_class_count)= c('repeat_class','total')
colnames(total_B_class_count) = c('repeat_class','total')
A_class_count = merge(missing_A_class_count,total_A_class_count, by= 'repeat_class')
B_class_count = merge(missing_B_class_count,total_B_class_count, by= 'repeat_class')
A_class_count=A_class_count %>% mutate(percent=n/total)
B_class_count=B_class_count %>% mutate(percent=n/total)
#plot for A
i = ggplot(A_class_count, aes(x=repeat_class, fill=repeat_class, y=percent)) +
geom_bar(stat = "identity") +
scale_fill_brewer(palette="Paired")+
theme(axis.text.x = element_text(angle = 25, hjust = 1))+
ggsave(paste(path_res,symbol_A,'percent_unmatched.png', sep = ""), height = 5, width =10)
#plot for B
j = ggplot(B_class_count, aes(x=repeat_class, fill=repeat_class, y=percent)) +
geom_bar(stat = "identity") +
scale_fill_brewer(palette="Paired")+
theme(axis.text.x = element_text(angle = 25, hjust = 1))+
ggsave(paste(path_res,symbol_B,'percent_unmatched.png', sep = ""), height = 5, width =10)