diff --git a/dev/flat_full.Rmd b/dev/flat_full.Rmd index 93da9e57fd7e2eccfa87d3b09158497abd6516bb..b3f61718e98c11165a41c2c8abb66bdce0896f99 100644 --- a/dev/flat_full.Rmd +++ b/dev/flat_full.Rmd @@ -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