-
Notifications
You must be signed in to change notification settings - Fork 0
/
2-generate_group_data.R
134 lines (107 loc) · 6.1 KB
/
2-generate_group_data.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
# This script takes the list of individual drugs and then sorts them into groups.
# Once sorted into groups, it generates an averaged signature, filters it and then
# gets the connected signatures
library(tidyverse)
library(glue)
source("pipeline.R")
names <- c("quine", "nib", "vir", "azt", "los")
quine_group <- c("Chloroquine", "Hydroxychloroquine")
nib_group <- c("Baricitinib", "Fedratinib", "Ruxolitinib")
vir_group <- c("Lopinavir", "Ritonavir")
azt_group <- c("Azithromycin")
los_group <- c("Losartan")
all_groups <- list(quine_group, nib_group, vir_group, azt_group, los_group)
sig_map_lists <- setdiff(list.files("maps"), c(list.files("maps", "Drug"), list.files("maps", "csv")))
sig_map_names <- str_match(sig_map_lists, "(.*)\\-Signature*")[,2]
sig_map_names <- sig_map_names[!is.na(sig_map_names)]
map_prefix <- "maps"
maps <- lapply(file.path(map_prefix, sig_map_lists), read_tsv)
names(maps) <- sig_map_names
process_group <- function(members, name, signature_map, cell_line, threshold = 0.85, library = "LIB_5") {
basepath <- file.path("data", cell_line)
sig_path <- file.path("data", "signatures", "group")
filtered_up_path <- file.path(basepath, "filtered", "group", "up")
filtered_down_path <- file.path(basepath, "filtered", "group", "down")
connected_up_path <- file.path(basepath, "connected", "group", "up")
connected_down_path <- file.path(basepath, "connected", "group", "down")
consensus_path <- file.path(basepath, "consensus", "group")
name_sig <- paste(name, cell_line, "signature", sep = "-")
name_filtered <- paste(name, threshold, "filtered", sep = "-")
name_connected <- paste(name, threshold, "connected", sep = "-")
name_consensus <- paste(name, threshold, "consensus", sep = "-")
file_sig <- generate_name(sig_path, name_sig, "tsv")
file_filtered_up <- generate_name(filtered_up_path, name_filtered, "tsv")
file_filtered_down <- generate_name(filtered_down_path, name_filtered, "tsv")
file_connected_up <- generate_name(connected_up_path, name_connected, "tsv")
file_connected_down <- generate_name(connected_down_path, name_connected, "tsv")
file_consensus <- generate_name(consensus_path, name_consensus, "tsv")
sigs <- signature_map %>%
filter(Drug %in% members) %>%
pull(SignatureId)
if (!is_empty(sigs)) {
print(glue("Processing {name} group for threshold {threshold}"))
if (!file.exists(file_sig)) {
sigs_data <- lapply(sigs, function(x) get_l1000_signature(x) %>% select(Name_GeneSymbol, Value_LogDiffExp))
group_sig <- reduce(sigs_data, inner_join, by = "Name_GeneSymbol") %>%
pivot_longer(cols = starts_with("Value")) %>%
group_by(Name_GeneSymbol) %>%
summarise(Value_LogDiffExp = mean(value)) %>%
write_tsv(file_sig)
} else {
print(glue("{file_sig} already exists"))
group_sig <- read_tsv(file_sig)
}
print(glue("Generating filtered signatures for {name} group"))
if (!file.exists(file_filtered_up)) {
filtered_up <- generate_filtered_signature(group_sig, direction = "up", threshold = threshold)
write_tsv(filtered_up, file_filtered_up)
} else {
print(glue("{file_filtered_up} already exists"))
filtered_up <- read_tsv(file_filtered_up)
}
if (!file.exists(file_filtered_down)) {
filtered_down <- generate_filtered_signature(group_sig, direction = "down", threshold = threshold)
write_tsv(filtered_down, file_filtered_down)
} else {
print(glue("{file_filtered_down} already exists"))
filtered_down <- read_tsv(file_filtered_down)
}
print(glue("Getting connected signatures for {name} group"))
if (!file.exists(file_connected_up)) {
connected_up <- get_concordant_signatures(filtered_up, library = library)
write_tsv(connected_up, file_connected_up)
} else {
print(glue("{file_connected_up} already exists"))
connected_up <- read_tsv(file_connected_up)
}
if (!file.exists(file_connected_down)) {
connected_down <- get_concordant_signatures(filtered_down, library = library)
write_tsv(connected_down, file_connected_down)
} else {
print(glue("{file_connected_down} already exists"))
connected_down <- read_tsv(file_connected_down)
}
print(glue("Generating consensus perturbagen list for {name} group"))
if (!file.exists(file_consensus)) {
consensus <- generate_consensus_signature(connected_up, connected_down, cell_line = "all")
write_tsv(consensus, file_consensus)
} else {
print(glue("{file_consensus} already exists"))
}
}
}
process_seed_groups <- function(groups, names, signature_map, cell_line, threshold = 0.85, library = "LIB_5") {
for (ind in 1:length(names)) {
print(glue("Processing {names[ind]} group of {cell_line}"))
process_group(members = groups[[ind]], name = names[[ind]], signature_map = signature_map, cell_line = cell_line, threshold = threshold, library = library)
}
}
cutoffs <- c(0, 0.26, 0.5, 0.85, 1)
a5491 <- sapply(cutoffs, process_seed_groups, groups = all_groups, names = names, signature_map = maps[[sig_map_names[1]]], cell_line = sig_map_names[1])
a5492 <- sapply(cutoffs, process_seed_groups, groups = all_groups, names = names, signature_map = maps[[sig_map_names[2]]], cell_line = sig_map_names[2])
ha1e2 <- sapply(cutoffs, process_seed_groups, groups = all_groups, names = names, signature_map = maps[[sig_map_names[3]]], cell_line = sig_map_names[3])
ht29 <- sapply(cutoffs, process_seed_groups, groups = all_groups, names = names, signature_map = maps[[sig_map_names[4]]], cell_line = sig_map_names[4])
mcf72 <- sapply(cutoffs, process_seed_groups, groups = all_groups, names = names, signature_map = maps[[sig_map_names[5]]], cell_line = sig_map_names[5])
pc3 <- sapply(cutoffs, process_seed_groups, groups = all_groups, names = names, signature_map = maps[[sig_map_names[6]]], cell_line = sig_map_names[6])
vcap1 <- sapply(cutoffs, process_seed_groups, groups = all_groups, names = names, signature_map = maps[[sig_map_names[7]]], cell_line = sig_map_names[7])
vcap2 <- sapply(cutoffs, process_seed_groups, groups = all_groups, names = names, signature_map = maps[[sig_map_names[8]]], cell_line = sig_map_names[8])