diff --git a/R_statistics_2022/R_stats_script.R b/R_statistics_2022/R_stats_script.R index 219944b..08cac83 100644 --- a/R_statistics_2022/R_stats_script.R +++ b/R_statistics_2022/R_stats_script.R @@ -868,7 +868,7 @@ plot( # To use spiec-easi for network inference, we will need to prepare the data into a specific R object type. # Also, since it uses clr-transformation to deal with compositionality, we need to use the filtered data set # that was already used in the RDA -physeqo_pro <-phyloseq( +physeqo_pro <- phyloseq( otu_table(otu_pro_filt, taxa_are_rows = T), tax_table(as.matrix(tax_pro[rownames(otu_pro_filt), ])) ) @@ -1001,7 +1001,7 @@ cluster.pick.rep <- lapply( names(cluster.pick.rep) <- paste0("M", 1:length(cluster.pick.rep)) # Look e.g. at taxonomic composition -i = 2 +i = 1 View(tax_pro[cluster.pick.rep[[i]], ]) # Correlation of eigengenes with environmental parameters @@ -1038,9 +1038,9 @@ plot( to = c(1, 10) ), vertex.label = NA, - vertex.color = ifelse(node_stats$degree > 15, "red", "blue"), + # vertex.color = ifelse(node_stats$degree > 15, "red", "blue"), # vertex.color = ifelse(node_stats$closeness > 0.045, "red", "blue"), - # vertex.color = ifelse(node_stats$betweenness > 5000, "red", "blue"), + vertex.color = ifelse(node_stats$betweenness > 5000, "red", "blue"), edge.color = "grey", edge.width = abs(E(adj.g.pos)$weight) * 5, main = "" diff --git a/R_statistics_2022/R_stats_slides.pdf b/R_statistics_2022/R_stats_slides.pdf index 88c1ed5..fbb953b 100644 Binary files a/R_statistics_2022/R_stats_slides.pdf and b/R_statistics_2022/R_stats_slides.pdf differ diff --git a/R_statistics_2022/machine_learning_slides.pdf b/R_statistics_2022/machine_learning_slides.pdf new file mode 100644 index 0000000..4b7fc8f Binary files /dev/null and b/R_statistics_2022/machine_learning_slides.pdf differ