figures: updated fig scripts (and some func.s in utils.R) to optimize figs for...

figures: updated fig scripts (and some func.s in utils.R) to optimize figs for submission (issue #127)

workflow_figures/scripts/fig_barrnap.R

@@ -62,16 +62,30 @@ for(sname in names(snakemake@config$samples)){
 xlim <- NULL
     FIGS[[sname]] <-
         plot_barrnap(TABS[[sname]]) +
-        labs(
-            title=LETTERS[which(names(TABS) == sname)],
-            subtitle=SAMPLE_NAMES[sname]
+        labs(title=SAMPLE_NAMES[sname]) +
+        theme(
+            plot.title=element_text(size=16, face="bold"),
+            plot.subtitle=element_text(size=16, face="italic"),
+            # legend
+            legend.title=element_text(size=16, face="bold"),
+            legend.text=element_text(size=16),
+            # strip
+            strip.text=element_text(size=14),
+            # axes
+            axis.title=element_text(size=16, color="black"),
+            axis.text.y=element_text(size=16, color="black"),
+            axis.text.x=element_text(size=16, color="black")
         )
+    # remove axis labels for first sub-plots (4 plots in a 2x2 layout)
+    if(which(names(SAMPLE_NAMES) == sname) < 3){
+        FIGS[[sname]] <- FIGS[[sname]] + theme(axis.text.x=element_blank())
+    }
 }
 
 # combine plots
 FIGS_ALL <- Reduce("+", FIGS) + plot_layout(ncol=2)
 
 # PDF
-pdf(snakemake@output$pdf, width=20, height=20)
+pdf(snakemake@output$pdf, width=20, height=14)
 print(FIGS_ALL)
 dev.off()
\ No newline at end of file

workflow_figures/scripts/fig_diamond_db.R

@@ -42,10 +42,21 @@ FIGS <- list()
 for(sname in names(snakemake@config$samples)){
 
 xlim <- NULL
-    FIGS[[sname]] <- plot_diamondDB_density(TABS[[sname]], col="qs_len_ratio", xlim=c(0, 3)) +
-    labs(
-        title=LETTERS[which(names(TABS) == sname)],
-        subtitle=SAMPLE_NAMES[sname]
+    FIGS[[sname]] <-
+        plot_diamondDB_density(TABS[[sname]], col="qs_len_ratio", xlim=c(0, 3)) +
+        labs(title=SAMPLE_NAMES[sname]) +
+        theme(
+            plot.title=element_text(size=16, face="bold"),
+            plot.subtitle=element_text(size=16, face="italic"),
+            # legend
+            legend.title=element_text(size=16, face="bold"),
+            legend.text=element_text(size=16),
+            # strip
+            strip.text=element_text(size=16),
+            # axes
+            axis.title=element_text(size=16, color="black"),
+            axis.text.y=element_text(size=16, color="black"),
+            axis.text.x=element_text(size=16, color="black", angle=0)
         )
 }
 
@@ -53,6 +64,6 @@ xlim <- NULL
 FIGS_ALL <- Reduce("+", FIGS) + plot_layout(ncol=2)
 
 # PDF
-pdf(snakemake@output$pdf, width=20, height=20)
+pdf(snakemake@output$pdf, width=20, height=14)
 print(FIGS_ALL)
 dev.off()
\ No newline at end of file

workflow_figures/scripts/fig_gdb_rgi_aro3004454_flye.R

@@ -77,7 +77,11 @@ custom_theme <-
     theme(
         panel.grid.major=element_blank(),
         panel.grid.minor=element_blank(),
-        legend.position="none"
+        legend.position="none",
+        # axes
+        axis.title=element_text(size=16, color="black"),
+        axis.text.y=element_text(size=16, color="black"),
+        axis.text.x=element_text(size=16, color="black")
     )
 
 # AA colors
@@ -117,7 +121,7 @@ p_cov  <-
         x=c(5547, 5547, 5780), y=c(2, -5, -5),
         label=levels(metat_cov_seqs$variable),
         hjust=c("left", "left", "right"),
-        size=4
+        size=5
     ) +
     # colors
     scale_fill_manual(values=aa_colors) +

workflow_figures/scripts/fig_mappability.R

@@ -44,23 +44,40 @@ for(sname in names(snakemake@config$samples)){
         TABS[[sname]] %>%
         filter(variable=="mapped_pct") %>%
         plot_mappability() +
-        labs(
-            title=LETTERS[which(names(TABS) == sname)],
-            subtitle=SAMPLE_NAMES[sname]
+        labs(title=SAMPLE_NAMES[sname]) +
+        theme(
+            plot.title=element_text(size=16, face="bold"),
+            plot.subtitle=element_text(size=16, face="italic"),
+            # legend
+            legend.title=element_text(size=16, face="bold"),
+            legend.text=element_text(size=16),
+            # strip
+            strip.text=element_text(size=16),
+            # axes
+            axis.title=element_text(size=16, color="black"),
+            axis.text.y=element_text(size=16, color="black"),
+            axis.text.x=element_text(size=16, color="black")
         )
+    # remove axis labels for first sub-plots (4 plots in a 2x2 layout)
+    if(which(names(SAMPLE_NAMES) == sname) < 3){
+        FIGS[[sname]] <- FIGS[[sname]] + theme(axis.text.x=element_blank())
+    }
 }
 
 # combine plots
 FIGS_ALL <- Reduce("+", FIGS) + plot_layout(ncol=2)
 
 # extra plot
-FIGS_gdb_metat <- TABS[["gdb_metat"]] %>% filter(variable=="mapped_pct") %>% plot_mappability()
+FIGS_gdb_metat <- 
+    TABS[["gdb_metat"]] %>% 
+    filter(variable=="mapped_pct") %>% 
+    plot_mappability()
 
 # PDF
-pdf(snakemake@output$pdf, width=20, height=14)
+pdf(snakemake@output$pdf, width=20, height=10)
 print(FIGS_ALL)
 dev.off()
 
-pdf(snakemake@output$pdf_gdb_metat, width=10, height=7)
+pdf(snakemake@output$pdf_gdb_metat, width=10, height=5)
 print(FIGS_gdb_metat)
 dev.off()
\ No newline at end of file

workflow_figures/scripts/fig_mash.R

@@ -51,13 +51,14 @@ for(sname in names(snakemake@config$samples)){
             scale="none",
             cluster_rows=HCLUST[[sname]],
             cluster_cols=HCLUST[[sname]],
-            display_numbers=TRUE, number_color="black", number_format="%.3f", fontsize_number=12,
+            display_numbers=TRUE, number_color="black", number_format="%.3f", fontsize_number=14,
+            fontsize=14,
             silent=TRUE
         )
     ) +
-    labs(
-        title=LETTERS[which(names(TABS) == sname)],
-        subtitle=SAMPLE_NAMES[sname]
+    labs(title=SAMPLE_NAMES[sname]) +
+    theme(
+        plot.title=element_text(size=16, face="bold")
     )
 }
 

workflow_figures/scripts/fig_mmseqs2.R

@@ -10,6 +10,8 @@ suppressMessages(library(testit)) # assertions
 suppressMessages(library(dplyr)) # tables
 suppressMessages(library(patchwork)) # combine plots
 suppressMessages(library(ggplotify)) # for as.ggplot
+# suppressMessages(library(grid)) # to combine upsetr plots
+# suppressMessages(library(gridExtra)) # to combine upsetr plots
 
 # custom
 source(snakemake@params$const)
@@ -43,16 +45,31 @@ FIGS <- list()
 for(sname in names(snakemake@config$samples)){
     FIGS[[sname]] <-
         as.ggplot(plot_mmseqs2_overlap(TABS[[sname]])) +
-    labs(
-        title=LETTERS[which(names(TABS) == sname)],
-        subtitle=SAMPLE_NAMES[sname]
-    )
+        labs(title=SAMPLE_NAMES[sname]) +
+        theme(plot.title=element_text(size=16, face="bold"))
 }
 
 # combine plots
 FIGS_ALL <- Reduce("+", FIGS) + plot_layout(ncol=2) #+ plot_annotation(tag_levels='A')
 
 # PDF
-pdf(snakemake@output$pdf, width=20, height=14)
+pdf(snakemake@output$pdf, width=20, height=12)
 print(FIGS_ALL)
 dev.off()
+
+# # individual plots
+# # solution for how to combine upsetR plots: https://stackoverflow.com/questions/57457651/upsetr-manually-order-set-intersections-to-align-multiple-upset-plots
+# FIGS <- list()
+# for(sname in names(snakemake@config$samples)){
+#     FIGS[[sname]] <- plot_mmseqs2_overlap(TABS[[sname]])
+#     print(FIGS[[sname]])
+#     grid.text(SAMPLE_NAMES[sname], x=0.05, y=0.95, gp=gpar(fontsize=16, fontface="bold"))
+#     grid.edit('arrange', name=sname)
+#     vp <- grid.grab()
+#     FIGS[[sname]] <- vp
+# }
+
+# # PDF
+# pdf(snakemake@output$pdf, width=20, height=12)
+# grid.arrange(grobs = FIGS, nrow=2)
+# dev.off()
\ No newline at end of file

workflow_figures/scripts/fig_prodigal.R

@@ -55,17 +55,32 @@ for(sname in names(snakemake@config$samples)){
 # individual plots
 FIGS <- list()
 for(sname in names(snakemake@config$samples)){
-    FIGS[[sname]] <- plot_prodigal2(TABS[[sname]]) +
-    labs(
-        title=LETTERS[which(names(TABS) == sname)],
-        subtitle=SAMPLE_NAMES[sname]
+    FIGS[[sname]] <-
+        plot_prodigal2(TABS[[sname]]) +
+        labs(title=SAMPLE_NAMES[sname]) +
+        theme(
+            plot.title=element_text(size=16, face="bold"),
+            plot.subtitle=element_text(size=16, face="italic"),
+            # legend
+            legend.title=element_text(size=16, face="bold"),
+            legend.text=element_text(size=16),
+            # strip
+            strip.text=element_text(size=16),
+            # axes
+            axis.title=element_text(size=16, color="black"),
+            axis.text.y=element_text(size=16, color="black"),
+            axis.text.x=element_text(size=16, color="black")
         )
+    # remove axis labels for first sub-plots (4 plots in a 2x2 layout)
+    if(which(names(SAMPLE_NAMES) == sname) < 3){
+        FIGS[[sname]] <- FIGS[[sname]] + theme(axis.text.x=element_blank())
+    }
 }
 
 # combine plots
 FIGS_ALL <- Reduce("+", FIGS) + plot_layout(ncol=2)
 
 # PDF
-pdf(snakemake@output$pdf, width=20, height=14)
+pdf(snakemake@output$pdf, width=20, height=8)
 print(FIGS_ALL)
 dev.off()
\ No newline at end of file

workflow_figures/scripts/fig_quast.R

@@ -40,17 +40,32 @@ for(sname in names(snakemake@config$samples)){
 # individual plots
 FIGS <- list()
 for(sname in names(snakemake@config$samples)){
-    FIGS[[sname]] <- plot_quast(TABS[[sname]]) +
-    labs(
-        title=LETTERS[which(names(TABS) == sname)],
-        subtitle=SAMPLE_NAMES[sname]
+    FIGS[[sname]] <-
+        plot_quast(TABS[[sname]]) +
+        labs(title=SAMPLE_NAMES[sname]) +
+        theme(
+            plot.title=element_text(size=16, face="bold"),
+            plot.subtitle=element_text(size=16, face="italic"),
+            # legend
+            legend.title=element_text(size=16, face="bold"),
+            legend.text=element_text(size=16),
+            # strip
+            strip.text=element_text(size=14),
+            # axes
+            axis.title=element_text(size=16, color="black"),
+            axis.text.y=element_text(size=16, color="black"),
+            axis.text.x=element_text(size=16, color="black")
         )
+    # remove axis labels for first sub-plots (4 plots in a 2x2 layout)
+    if(which(names(SAMPLE_NAMES) == sname) < 3){
+        FIGS[[sname]] <- FIGS[[sname]] + theme(axis.text.x=element_blank())
+    }
 }
 
 # combine plots
 FIGS_ALL <- Reduce("+", FIGS) + plot_layout(ncol=2)
 
 # PDF
-pdf(snakemake@output$pdf, width=20, height=20)
+pdf(snakemake@output$pdf, width=20, height=14)
 print(FIGS_ALL)
 dev.off()
\ No newline at end of file

workflow_figures/scripts/fig_rgi.R

@@ -9,7 +9,8 @@ sink(file=file(snakemake@log[[1]], open="wt"), type=c("output", "message"))
 suppressMessages(library(testit)) # assertions
 suppressMessages(library(dplyr)) # tables
 suppressMessages(library(patchwork)) # combine plots
-suppressMessages(library(ggplotify)) # for as.ggplot
+suppressMessages(library(grid)) # to combine upsetr plots
+suppressMessages(library(gridExtra)) # to combine upsetr plots
 
 # custom
 source(snakemake@params$const)
@@ -47,27 +48,36 @@ FIGS_o <- list()
 for(sname in names(TABS)){
     FIGS_c[[sname]] <-
         plot_rgi_counts_total(proc_rgi(TABS[[sname]])$aggr) +
-        labs(
-            title=LETTERS[which(names(TABS) == sname)],
-            subtitle=SAMPLE_NAMES[sname]
-        )
-    FIGS_o[[sname]] <-
-        as.ggplot(plot_rgi_overlap(TABS[[sname]], "strict", "ARO")) +
-        labs(
-            title=LETTERS[which(names(TABS) == sname)],
-            subtitle=SAMPLE_NAMES[sname]
+        labs(title=SAMPLE_NAMES[sname]) +
+        theme(
+            plot.title=element_text(size=16, face="bold"),
+            plot.subtitle=element_text(size=16, face="italic"),
+            # legend
+            legend.title=element_text(size=16, face="bold"),
+            legend.text=element_text(size=16),
+            # strip
+            strip.text=element_text(size=14),
+            # axes
+            axis.title=element_text(size=16, color="black"),
+            axis.text.y=element_text(size=16, color="black"),
+            axis.text.x=element_text(size=16, color="black")
         )
+    FIGS_o[[sname]] <- plot_rgi_overlap(TABS[[sname]], "strict", "ARO")
+    print(FIGS_o[[sname]])
+    grid.text(SAMPLE_NAMES[sname], x=0.05, y=0.95, gp=gpar(fontsize=16, fontface="bold"))
+    grid.edit('arrange', name=sname)
+    vp <- grid.grab()
+    FIGS_o[[sname]] <- vp
 }
 
 # combine plots
 FIGS_ALL_c <- Reduce("+", FIGS_c) + plot_layout(ncol=3)
-FIGS_ALL_o <- Reduce("+", FIGS_o) + plot_layout(ncol=3)
 
 # PDF
-pdf(snakemake@output$pdf_c, width=30, height=7)
+pdf(snakemake@output$pdf_c, width=20, height=5)
 print(FIGS_ALL_c)
 dev.off()
 
-pdf(snakemake@output$pdf_o, width=30, height=7)
-print(FIGS_ALL_o)
+pdf(snakemake@output$pdf_o, width=20, height=5)
+grid.arrange(grobs=FIGS_o, ncol=3)
 dev.off()
\ No newline at end of file

workflow_report/scripts/utils.R

@@ -503,9 +503,11 @@ plot_rgi_overlap <- function(df, ctype, col){
         # number of sets to plot
         nsets=length(ASM_TOOL_NAMES),
         # y-label title
-        mainbar.y.label=sprintf("Intersection size (%s hits, %s)", ctype, col),
+        mainbar.y.label=sprintf("Intersection size\n(%s hits, %s)", ctype, col),
         # text size: intersection size title, intersection size tick labels, set size title, set size tick labels, set names, numbers above bars
-        text.scale = c(1.2, 1.2, 1.2, 1.2, 1.2, 1.2)#,
+        text.scale=c(2, 2, 1.8, 1.3, 2, 2),
+        # ratio between matrix plot and main bar plot
+        mb.ratio=c(0.65,0.35),
         # colors
         # set.metadata=list(
         #     data=data.frame(
@@ -653,10 +655,12 @@ plot_mmseqs2_overlap <- function(df, topN=20){
         order.by="freq",
         decreasing=TRUE,
         # titles
-        mainbar.y.label="Total number of proteins in clusters",
-        sets.x.label="Total number of proteins per assembly",
+        mainbar.y.label="Total number of proteins\nin clusters",
+        sets.x.label="Total number of proteins\nper assembly",
         # text size: intersection size title, intersection size tick labels, set size title, set size tick labels, set names, numbers above bars
-        text.scale = c(1.2, 1.2, 1.2, 1.2, 1.2, 1),
+        text.scale=c(2, 1.6, 1.8, 1.3, 2, 1),
+        # ratio between matrix plot and main bar plot
+        mb.ratio=c(0.6,0.4),
         # highlight those w/ only one set
         queries=c(
             # unique proteins