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Verified Commit e08973db authored by Laurent Modolo's avatar Laurent Modolo
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clean flexmix code

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......@@ -308,7 +308,7 @@ plot_proba <- function(x, proba, sex = "XY") {
proba_m = proba[, 3],
clust_proba = rgb(proba_f, proba_m, proba_a, maxColorValue = 1),
) %>%
sample_n(100000) %>%
sample_n(min(c(100000, nrow(x)))) %>%
ggplot(aes(x = count_m, y = count_f, color = clust_proba)) +
geom_point() +
scale_color_identity() +
......@@ -321,7 +321,7 @@ plot_proba <- function(x, proba, sex = "XY") {
proba_f = proba[, 2],
clust_proba = rgb(proba_f, 0, proba_a, maxColorValue = 1),
) %>%
sample_n(100000) %>%
sample_n(min(c(100000, nrow(x)))) %>%
ggplot(aes(x = count_m, y = count_f, color = clust_proba)) +
geom_point() +
scale_color_identity() +
......@@ -525,35 +525,6 @@ data %>%
plot_proba(model_XY$proba)
```
```{r clustering_XY_flexmix}
library(flexmix)
m_xy <- flexmix(
log1p(count_m) ~ I(log1p(count_f) + I(log1p(count_f))),
k = 3,
data = data %>%
dplyr::select(count_m, count_f),
# model = FLXglm(family = "poisson")
)
summary(m_xy)
parameters(m_xy, component = 1)
parameters(m_xy, component = 2)
parameters(m_xy, component = 3)
plot(m_xy)
rm_xy <- refit(m_xy)
summary(rm_xy)
data %>%
mutate(
proba1 = m_xy@posterior$scaled[, 1],
proba2 = m_xy@posterior$scaled[, 2],
proba3 = m_xy@posterior$scaled[, 3]
) %>%
pivot_longer(cols = c(proba1, proba2, proba3)) %>%
ggplot(aes(x = log1p(count_m), y = log1p(count_f), color = value)) +
geom_point() +
facet_wrap(~name) +
theme_bw()
```
# clustering XO
```{r clustering_XO}
......@@ -568,29 +539,6 @@ data %>%
plot_proba(model_XO$proba, sex = "X0")
```
```{r clustering_X0_flexmix}
m_xo <- flexmix(
count_m ~ I(count_f + I(count_f)),
k = 2,
data = data %>%
dplyr::select(count_m, count_f)
)
summary(m_xo)
parameters(m_xo, component = 1)
parameters(m_xo, component = 2)
plot(m_xo)
rm_xo <- refit(m_xo)
summary(rm_xo)
data %>%
mutate(
proba1 = m_xo@posterior$scaled[, 1],
proba2 = m_xo@posterior$scaled[, 2],
) %>%
ggplot(aes(x = count_m, y = count_f, color = proba2)) +
geom_point() +
theme_bw()
```
# LRT
## For XY
......
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