-
Notifications
You must be signed in to change notification settings - Fork 0
/
benchmark_interpretation.R
272 lines (220 loc) · 10.2 KB
/
benchmark_interpretation.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
source("utils.R")
# CTCL
# Load and format Kasumi results
misty.results <- read_rds("CTCLct400.rds")
sm.repr <- sm_labels(misty.results, 0.4, 0.9)
sm.repr.ext <- sm_labels(misty.results, 0.4, 0.9, freq = FALSE)
freq_all_clusters <- sapply(sm.repr.ext,
function(x) x %>%
select(-id, -x, -y) %>%
colSums)
# Compile cluster stats
cluster_stats <- data.frame(samples = rowSums(freq_all_clusters > 0))
cluster_stats$names <- sm.repr.ext[[1]] %>%
select(-id, -x, -y) %>%
names
cluster_stats$windows <- rowSums(freq_all_clusters)
cluster_stats$selected <- cluster_stats$names %in% names(sm.repr)
# Number of samples, pop size per class, number of draws
expected_samples_for_x_windows <- function(x, repet = 50000){
X <- rmvhyper(repet, sapply(sm.repr.ext, nrow), x)
X <- rowSums(X > 0)
return(quantile(x = X, probs = c(0.1,0.5,0.9)))
}
with_seed(
42,
expected_samples_per_windows <- sapply(min(cluster_stats$windows):max(cluster_stats$windows),
expected_samples_for_x_windows)
)
expected_samples_per_windows <- data.frame(t(expected_samples_per_windows))
expected_samples_per_windows$windows <- min(cluster_stats$windows):max(cluster_stats$windows)
expected_samples_per_windows$selected <- "Expectation"
lymph <- read_csv("data/LymphomaCODEX/single_cells.csv")
spots <- lymph %>%
filter(Groups %in% c(1, 2)) %>%
pull(Spots) %>%
unique()
outcome <- lymph %>%
filter(Groups %in% c(1, 2)) %>%
group_by(Spots, Patients) %>%
summarize(Groups = Groups[1], .groups = "drop")
freq.expr <- sm.repr %>%
left_join(outcome %>%
mutate(Spots = as.character(Spots)), by = c("id" = "Spots")) %>%
rename(target = Groups) %>%
mutate(target = as.factor(make.names(target))) %>%
select(-id, -Patients)
reliance <- model_reliance(freq.expr)
ggsave("CTCLreliance_interpretation.pdf", last_plot())
cluster_stats$names <- str_remove(string = cluster_stats$names, pattern = "...")
cluster_stats <- cluster_stats %>%
left_join(reliance, by = join_by(names == Cluster))
# Label clusters only if they have a significant sMR
cluster_stats$label <- ifelse(abs(cluster_stats$sMR) > 1, cluster_stats$names, NA)
# and if they have an unusual number of samples compared to their number of windows
lowsamples <- (cluster_stats %>%
left_join(expected_samples_per_windows, by = "windows") %>%
mutate(lowsamples = X10. > samples))$lowsamples
cluster_stats$label <- ifelse(lowsamples, cluster_stats$label, NA)
# Plot and save
gp <- ggplot(cluster_stats, aes(y = samples, x = windows, color = sMR)) +
geom_point() +
geom_hline(yintercept = 5, lty = 2, color = "gray50") +
theme_classic() +
geom_line(data = expected_samples_per_windows,
aes(y = X50., x = windows), color = "gray50") +
geom_line(data = expected_samples_per_windows,
aes(y = X90., x = windows), color = "gray75", lty = 2) +
geom_line(data = expected_samples_per_windows,
aes(y = X10., x = windows), color = "gray75", lty = 2) +
geom_text_repel(aes(label = label)) +
ggtitle("Frequency of window clusters") +
xlab("Number of windows") +
ylab("Number of samples") +
scale_color_steps2(low = "#008837", mid = "white", high = "#7b3294", na.value="gray75")
ggsave("CTCLct400_cluster_frequency.pdf", gp, height = 5, width = 5)
# For all the selected clusters
# (Non-randomly spread across samples and useful for classification)
contig_scores <- cluster_stats$label %>%
na.omit %>%
sapply(function(x) na.omit(moran_score(sm.repr.ext, paste0("...", x), stride = 200, pval = TRUE)), simplify = FALSE)
contig_clusters <- lapply(names(contig_scores), function(name) {
rep(name, length(na.omit(unlist(contig_scores[[name]])))/3)
})
contiguity_df <- data.frame(clusters = rep(unlist(contig_clusters), 2))
unlist_scores <- na.omit(unlist(contig_scores))
contiguity_df$scores <- c(unlist_scores[3*1:(length(unlist_scores)/3) - 1], unlist_scores[3*1:(length(unlist_scores)/3) - 2])
contiguity_df$type <- rep(c("Expected", "Observed"), each = length(unlist(contig_clusters)))
contiguity_pval <- unlist_scores[3*1:(length(unlist_scores)/3)]
pval_df <- data.frame(pval = contiguity_pval, clusters = unlist(contig_clusters))
pval_df <- pval_df %>% group_by(clusters) %>%
mutate(cor_p = p.adjust(pval, "bonferroni")) %>%
summarize(mincorp = min(cor_p)) %>%
mutate(mincorp = p.adjust(mincorp, "BH"))
pval_df$text <- paste("p =", signif(pval_df$mincorp, 3))
# Define the color mapping and the plot scales
color_mapping <- c("Expected" = "#CCCCCC", "Observed" = "#8FA1CC")
xmin <- min(contiguity_df$scores)
xmax <- max(contiguity_df$scores) + 0.2
gp <- ggplot(contiguity_df, aes(x = clusters, y = scores)) +
geom_violin(aes(fill = type), draw_quantiles = c(0.25, 0.5, 0.75), scale = "width") +
scale_fill_manual(values = color_mapping) +
theme_classic() +
xlab("Clusters") + ylab("Moran's I") +
coord_flip() +
ylim(xmin,xmax) +
geom_text(aes(label = text), data = pval_df, size = 3, y = xmax - 0.1) +
guides(fill = guide_legend("I values", reverse = TRUE))
ggsave("CTCLct400_cluster_moran_signif.pdf", gp, height = 5, width = 5)
# IMC
misty.results <- read_rds("BCexpr200.rds")
bmeta <- read_csv("data/BCIMC/Basel_PatientMetadata.csv")
with_seed(
1,
cores <- bmeta %>%
filter(
diseasestatus == "tumor",
response %in% c("Sensitive", "Resistant"),
clinical_type == "HR+HER2-", Subtype == "PR+ER+"
) %>%
group_by(response) %>%
slice_sample(n = 15) %>%
pull(core)
)
resp <- bmeta %>%
filter(core %in% cores) %>%
select(core, response)
sm.repr <- sm_labels(misty.results, 0.3, 0.8)
sm.repr.ext <- sm_labels(misty.results, 0.3, 0.8, freq = FALSE)
freq.sm <- sm.repr %>%
left_join(resp, by = c("id" = "core")) %>%
rename(target = response) %>%
mutate(target = as.factor(make.names(target))) %>%
select(-id)
freq_all_clusters <- sapply(sm.repr.ext,
function(x) x %>%
select(-id, -x, -y) %>%
colSums)
reliance <- model_reliance(freq.sm)
ggsave("BCreliance_interpretation.pdf", last_plot())
# Compile cluster stats
cluster_stats <- data.frame(samples = rowSums(freq_all_clusters > 0))
cluster_stats$names <- sm.repr.ext[[1]] %>%
select(-id, -x, -y) %>%
names
cluster_stats$windows <- rowSums(freq_all_clusters)
cluster_stats$selected <- cluster_stats$names %in% names(sm.repr)
# Number of samples, pop size per class, number of draws
expected_samples_for_x_windows <- function(x, repet = 50000){
X <- rmvhyper(repet, sapply(sm.repr.ext, nrow), x)
X <- rowSums(X > 0)
return(quantile(x = X, probs = c(0.1,0.5,0.9)))
}
with_seed(
42,
expected_samples_per_windows <- sapply(min(cluster_stats$windows):max(cluster_stats$windows),
expected_samples_for_x_windows)
)
expected_samples_per_windows <- data.frame(t(expected_samples_per_windows))
expected_samples_per_windows$windows <- min(cluster_stats$windows):max(cluster_stats$windows)
expected_samples_per_windows$selected <- "Expectation"
cluster_stats$names <- str_remove(string = cluster_stats$names, pattern = "...")
cluster_stats <- cluster_stats %>%
left_join(reliance, by = join_by(names == Cluster))
# Label clusters only if they have a significant sMR
cluster_stats$label <- ifelse(abs(cluster_stats$sMR) > 1, cluster_stats$names, NA)
# and if they have an unusual number of samples compared to their number of windows
lowsamples <- (cluster_stats %>%
left_join(expected_samples_per_windows, by = "windows") %>%
mutate(lowsamples = X10. > samples))$lowsamples
cluster_stats$label <- ifelse(lowsamples, cluster_stats$label, NA)
# Plot and save
gp <- ggplot(cluster_stats, aes(y = samples, x = windows, color = sMR)) +
geom_point() +
geom_hline(yintercept = 5, lty = 2, color = "gray50") +
theme_classic() +
geom_line(data = expected_samples_per_windows,
aes(y = X50., x = windows), color = "gray50") +
geom_line(data = expected_samples_per_windows,
aes(y = X90., x = windows), color = "gray75", lty = 2) +
geom_line(data = expected_samples_per_windows,
aes(y = X10., x = windows), color = "gray75", lty = 2) +
geom_text_repel(aes(label = label)) +
ggtitle("Frequency of window clusters") +
xlab("Number of windows") +
ylab("Number of samples") +
scale_color_steps2(low = "#008837", mid = "white", high = "#7b3294", na.value="gray75")
ggsave("BCexpr200_cluster_frequency.pdf", gp, height = 5, width = 5)
# For all the selected clusters
# (Non-randomly spread across samples and useful for classification)
contig_scores <- cluster_stats$label %>%
na.omit %>%
sapply(function(x) na.omit(moran_score(sm.repr.ext, paste0("...", x), stride = 150, pval = TRUE)), simplify = FALSE)
contig_clusters <- lapply(names(contig_scores), function(name) {
rep(name, length(na.omit(unlist(contig_scores[[name]])))/3)
})
contiguity_df <- data.frame(clusters = rep(unlist(contig_clusters), 2))
unlist_scores <- na.omit(unlist(contig_scores))
contiguity_df$scores <- c(unlist_scores[3*1:(length(unlist_scores)/3) - 1], unlist_scores[3*1:(length(unlist_scores)/3) - 2])
contiguity_df$type <- rep(c("Expected", "Observed"), each = length(unlist(contig_clusters)))
contiguity_pval <- unlist_scores[3*1:(length(unlist_scores)/3)]
pval_df <- data.frame(pval = contiguity_pval, clusters = unlist(contig_clusters))
pval_df <- pval_df %>% group_by(clusters) %>%
mutate(cor_p = p.adjust(pval, "bonferroni")) %>%
summarize(mincorp = min(cor_p)) %>%
mutate(mincorp = p.adjust(mincorp, "BH"))
pval_df$text <- paste("p =", signif(pval_df$mincorp, 3))
# Define the color mapping and the plot scales
color_mapping <- c("Expected" = "#CCCCCC", "Observed" = "#8FA1CC")
xmin <- min(contiguity_df$scores)
xmax <- max(contiguity_df$scores) + 0.2
gp <- ggplot(contiguity_df, aes(x = clusters, y = scores)) +
geom_violin(aes(fill = type), draw_quantiles = c(0.25, 0.5, 0.75), scale = "width") +
scale_fill_manual(values = color_mapping) +
theme_classic() +
xlab("Clusters") + ylab("Moran's I") +
coord_flip() +
ylim(xmin,xmax) +
geom_text(aes(label = text), data = pval_df, size = 3, y = xmax - 0.1) +
guides(fill = guide_legend("I values", reverse = TRUE))
ggsave("BCexpr200_cluster_moran_signif.pdf", gp, height = 5, width = 5)