Graph for time and size of OTUs

analysis_benchmark_lbm_seq.R

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+library(here)
+library(stringr)
+library(tidyverse)
+library(phyloseq)
+library(biomformat)
+source("utils.R")
+the_data <- import_biom("data/mach/kinetic.biom")
+per_taxa_networks <- collapse_otu_at_taxo(the_data)
+otu_df <- sapply(per_taxa_networks, nrow) %>%
+    data.frame() %>%
+    rownames_to_column() %>%
+    rename(Nb_OTU = ".", Rank = "rowname")
+
+
+flist <- list.files(here("results", "lbm-seq"), full.names = TRUE, pattern = ".Rds")
+
+para_flist <- grepv(pattern = "para.Rds", flist)
+seq_flist <- grepv(pattern = "seq.Rds", flist)
+notrans_flist <- grepv(pattern = "notrans.Rds", flist)
+
+bench_df <- do.call("rbind", lapply(flist, function(file) readRDS(file)$benchmark))
+
+bench_df <- bench_df %>%
+    mutate(expr = as.character(expr)) %>%
+    separate_wider_regex(cols = "expr", patterns = c(Rank = "Rank[0-9]", type = "para|seq|notrans")) %>%
+    mutate(Rank = as.factor(Rank), type = as.factor(type)) %>%
+    left_join(otu_df, by = "Rank") %>%
+    mutate(Rank = as.factor(Rank), type = as.factor(type))
+
+
+
+levels(bench_df$Rank) <- c("Phylum", "Class", "Order", "Family", "Genus")
+
+library(ggplot2)
+
+coeff <- 220000000000
+
+ggplot(bench_df, aes(x = Rank, col = type)) +
+    geom_boxplot(aes(y = time)) +
+    geom_point(aes(y = coeff * Nb_OTU, size = Nb_OTU), shape = 13) +
+    scale_color_manual(values = c("#363634", "#009E73", "#CC79A7"), labels = c("No transfer", "Parallelized", "Sequential")) +
+    scale_y_continuous(sec.axis = sec_axis(~ . / coeff, name = "Number of OTUs")) +
+    labs(size = "Number of OTUs", color = "Algorithm Type", y = "Time (seconds)") +
+    theme_minimal()