DciA figures implementation

R/dciaViz.R

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+library(tidyverse)
+library(aplot)
+library(ape)
+library(tidytree)
+library(seqinr)
+library(msa)
+library(htmltools)
+library(data.table)
+
+# figures 2 and 4 from DciA paper, https://journals.asm.org/doi/epub/10.1128/jb.00163-22
+
+df_shared <- function(job_dir) {
+  df <- read_tsv(file.path(job_dir, "./query_data/query_data.ipr_domarch.tsv")) # /data/scratch/jburke/dcia/all_seqs_full_with_mobi_ipr_distinct_2.tsv
+
+  df$Name <- str_replace_all(df$Name, "\\[", "")
+  df$QueryName <- df$Name
+
+  df <- df %>% filter(Lineage != "") %>% drop_na(Lineage)
+  df <- df %>% mutate(DomArch.Pfam = gsub("_[0-9]{1,2}", "", DomArch.Pfam)) %>%
+    mutate(DomArch.Pfam = str_replace(DomArch.Pfam, "TPR\\+.*", paste0("TPR(", str_count(DomArch.Pfam, "TPR"), ")"))) %>%
+    mutate(DomArch.Pfam = str_replace(DomArch.Pfam, "DciA\\+DciA\\+DciA\\+DciA", "DciA(4)"))
+
+  return(df)
+}
+
+dcia_figure2 <- function(job_dir) {
+  ## Figure 2
+  # Fig 2a length box plot of DciA only bac
+
+  df <- df_shared(job_dir)
+
+  df_fig2 <- df %>%
+    filter(DomArch.Pfam == "DciA") %>%
+    filter(grepl("Bacteria>", Lineage)) %>%
+    filter(!grepl("Candidatus", Lineage)) %>%
+    filter(!grepl("candidate", Lineage)) %>%
+    distinct(AccNum, .keep_all = TRUE) %>%
+    drop_na(pfam_start)
+
+  df_fig2$domainLength <- df_fig2$pfam_stop - df_fig2$pfam_start
+  df_fig2$fromStart <- df_fig2$pfam_start
+  df_fig2$fromEnd <- df_fig2$seq_length - df_fig2$pfam_stop
+  df_fig2$seqLength <- df_fig2$seq_length
+  df_fig2 <- df_fig2 %>%
+    pivot_longer(c(seqLength, fromStart, fromEnd), names_to = "Type", values_to = "length")
+  df_fig2$Type <- factor(df_fig2$Type, levels = c("seqLength", "fromStart", "fromEnd"))
+  df_fig2_stats <- df_fig2 %>%
+    group_by(Type) %>%
+    mutate(med = median(length), twent = quantile(length, c(0.25)), sev = quantile(length, c(0.75)))
+
+  fig_2a <- ggplot(df_fig2, aes(x=Lineage, length)) +
+    geom_boxplot(outlier.alpha = 0.5, outlier.color = "black") +
+    labs(y = "Length", x = "Lineage") +
+    theme_minimal() +
+    theme(axis.text.x = element_text(angle = 90, vjust = 0.8, hjust=1),
+          panel.grid.major = element_blank(),
+          panel.grid.minor = element_blank(),
+          axis.line = element_line(colour = "black"),
+          axis.ticks = element_line(colour = "black"),
+          plot.background = element_rect("white", size = 0),
+          text = element_text(size = 18), panel.border = element_blank()) +
+    facet_grid(Type ~ . , scales = "free") +
+    geom_hline(data = df_fig2_stats, aes(yintercept = med), color = "blue") +
+    geom_hline(data = df_fig2_stats, aes(yintercept = twent), color = "blue", alpha = 0.5) +
+    geom_hline(data = df_fig2_stats, aes(yintercept = df_fig2_stats$sev), color = "blue", alpha = 0.5)
+
+  return(fig_2a)
+}
+
+dcia_figure4 <- function(job_dir, save_figs=FALSE) {
+  df <- df_shared(job_dir)
+
+  df_bact <- df %>% filter(grepl("Bacteria>", Lineage))
+
+  df_bact <- df_bact %>%
+    filter(grepl("Bacteria", Lineage)) %>%
+    drop_na(AccNum) %>%
+    filter(!grepl("candidate", Lineage)) %>%
+    filter(!grepl("Candidatus", Lineage)) %>%
+    filter(!grepl("candidate", Species)) %>%
+    filter(!grepl("Candidat", Species)) %>%
+    filter(!grepl("uncultur", Species))
+
+  df_bact$DomArch.Pfam <- str_replace_all(df_bact$DomArch.Pfam , "Hydrolase\\+DciA", "HAD_2+DciA")
+
+  ## FIGURE 4
+  # Fig 4a stacked bar plot of lineage
+  df_fig4 <- df_bact %>% filter(DomArch.Pfam == "DciA")%>% drop_na(seq_length)
+  df_fig4$fromEnd <- df_fig4$seq_length - df_fig4$pfam_stop
+  df_fig4$fromStart <- df_fig4$pfam_start
+  df_fig4$group <- ""
+  df_fig4$group[which(df_fig4$fromStart >= 14 & df_fig4$fromEnd < 14)] <- 1
+  df_fig4$group[which(df_fig4$fromEnd >= 14 &  df_fig4$fromStart < 14)] <- 2
+  df_fig4$group[which(df_fig4$fromEnd >= 14 &  df_fig4$fromStart >= 14)] <- 3
+  df_fig4$group[which(df_fig4$group == "")] <- 4
+  write_tsv(df_fig4, "dcia_figs/fig4/cln_with_groups.tsv")
+
+  stacked_fig4a <- stacked_lin_plot(df_fig4, column = "group", cutoff = 100,
+                              xlabel = "Group", legend.position = c(0.7,0.3),
+                              legend.cols = 2)
+
+  stacked_fig4a_nolegend <- stacked_lin_plot(df_fig4, column = "group", cutoff = 100,
+                              xlabel = "Group", legend.position = c(0.7,0.3),
+                              legend.cols = 2, legend = FALSE)
+
+  # Fig 4b
+  df_fig4_b <- df_fig4 %>% filter(Lineage == "Bacteria>Proteobacteria" | Lineage == "Bacteria>Actinobacteria" | Lineage == "Bacteria>Bacteroidetes")
+  stacked_fig4b <- stacked_lin_plot(df_fig4_b, column = "group",
+                              Lineage_col = "Lineage_short", cutoff = 100,
+                              xlabel = "Group", legend.position = c(0.7,0.4),
+                              legend.cols = 2, reduce_lineage = FALSE)
+                              Lineage_col = "Lineage_short", cutoff = 100,
+                              xlabel = "Group", legend.position = c(0.7,0.4),
+                              legend.cols = 2, reduce_lineage = FALSE, legend = FALSE)
+
+  # Fig 4c
+  df_fig4_c <- df_fig4 %>%
+    filter(Lineage != "Bacteria>Proteobacteria" & Lineage != "Bacteria>Actinobacteria" & Lineage != "Bacteria>Bacteroidetes")
+  stacked_fig4c <- stacked_lin_plot(df_fig4_c, column = "group", cutoff = 100,
+                              xlabel = "Group", legend.position = c(0.7,0.15),
+                              legend.cols = 4)
+  stacked_fig4c_nolegend <- stacked_lin_plot(df_fig4_b, column = "group", cutoff = 100,
+                              xlabel = "Group", legend.position = c(0.7,0.15),
+                              legend.cols = 4, legend = FALSE)
+
+  if (save_figs) {
+    ggsave("dcia_figs/fig4/4a.png", stacked_fig4a, dpi = 400, device = "png", height = 15, width = 15)
+    ggsave("dcia_figs/fig4/4_no_legend.png", stacked_fig4a_nolegend, dpi = 400, device = "png", height = 15, width = 15)
+
+    ggsave("dcia_figs/fig4/4b.png", stacked_fig4b, dpi = 400, device = "png", height = 15, width = 15) stacked_fig4b_nolegend <- stacked_lin_plot(df_fig4_b, column = "group",
+    ggsave("dcia_figs/fig4/4b_no_legend.png", stacked_fig4b_nolegend, dpi = 400, device = "png", height = 15, width = 15)
+
+    ggsave("dcia_figs/fig4/4c.png", stacked_fig4c, dpi = 400, device = "png", height = 15, width = 15)
+    ggsave("dcia_figs/fig4/4c_no_legend.png", stacked_fig4c_nolegend, dpi = 400, device = "png", height = 15, width = 15)
+  }
+
+  return(
+    list(
+      stacked_fig4a = stacked_fig4a,
+      stacked_fig4a_nolegend = stacked_fig4a_nolegend,
+
+      stacked_fig4b = stacked_fig4b,
+      stacked_fig4b_nolegend = stacked_fig4b_nolegend,
+
+      stacked_fig4c = stacked_fig4c,
+      stacked_fig4c_nolegend = stacked_fig4c_nolegend
+    )
+  )
+}