diff --git a/lbm_phyloseq_test.R b/lbm_phyloseq_test.R new file mode 100644 index 0000000..918d16b --- /dev/null +++ b/lbm_phyloseq_test.R @@ -0,0 +1,53 @@ +library(phyloseq) +library(ggplot2) +library(sbm) +library(biomformat) + +# data("enterotype") +# data("mach") +data <- import_biom("data/chaillou/chaillou.biom") +net_table <- otu_table(data) +dim(net_table) + +nb_inter <- sum(net_table > 0) +all_possible_inter <- nrow(net_table) * ncol(net_table) +(density <- nb_inter / all_possible_inter) + +res <- estimateBipartiteSBM(net_table, dimLabels = c("OTU", "Sample"), model = "poisson") +res_t <- estimateBipartiteSBM(t(net_table), dimLabels = rev(c("OTU", "Sample"))) + +plot(res, type = "data") + +plot(res_t, type = "data") + +sdCol <- function(matrix) { + sapply(seq_len(ncol(matrix)), function(col) sd(matrix[, col])) +} + +t_net_table <- t(net_table) +std_otu <- sdCol(t_net_table) +mean_otu <- rowMeans(net_table) + +stats_df <- data.frame(otu = rownames(net_table), mean = mean_otu, std = std_otu, var = std_otu^2) + +ggplot(stats_df, aes(x = mean, y = var)) + + geom_line() + + geom_point() + + geom_abline(slope = 1, color = "red") + + scale_y_log10() + + scale_x_log10() + + ggtitle("OTU for log(mean) = log(var)") + +ggplot(stats_df, aes(x = mean, y = var / mean)) + + geom_line() + + geom_point() + + geom_hline(yintercept = 1, color = "red") + + ggtitle("OTU for f(mean) = var/mean = 1") + +ggplot(stats_df, aes(x = 1 / mean, y = var / mean^2)) + + geom_line() + + geom_point() + + geom_abline(slope = 1, color = "red") + + scale_y_log10() + + scale_x_log10() + + ggtitle("OTU for log(1/mean) = log(var/mean^2)")