Revised top n genera figures for all markers

Revision request, reknitted as a result

analysis/FITS2/FITS2_Analysis_pipeline_v4-3.Rmd

@@ -719,7 +719,7 @@ set$ps.topnTax <- cuphyr::abundant_tax_physeq(ps.trans, lvl = set$taxlvl,
 set$my_scale_fill <- my_scale_fill
 
 
-set$topntax_tbl <- psmelt(set$ps.topnTax) %>% 
+set$topntax_tb <- psmelt(set$ps.topnTax) %>% 
                     as_tibble() %>%
                     left_join(set$alpha_div_ps_trans, by = "Sample") %>% 
                     select(Genus, Alias, ndvi, Abundance, Shannon) %>%
@@ -729,16 +729,28 @@ set$topntax_tbl <- psmelt(set$ps.topnTax) %>%
                     arrange(ndvi) %>%
                     mutate(ndvi_rank = c(1:length(ndvi))) 
                     
+set$other <- set$topntax_tb %>% 
+  group_by(Alias) %>% 
+  summarise(sumabu = sum(Abundance)) %>% 
+  mutate(Genus = 'Other', Abundance = 1-sumabu) %>% 
+  select(-sumabu)
+
+set$topntax_tbl <- bind_rows(set$topntax_tb, set$other) %>% 
+  mutate(Genus = factor(Genus, levels = c(
+    sort(unique(set$topntax_tb$Genus)),
+    "Other")
+    ))
 
 plots$topn_tax_custom <- ggplot(set$topntax_tbl, aes(x = fct_reorder(Alias, ndvi),
                            y = Abundance,
                            fill = Genus)) + 
-                           #title = paste0("Top ", set$top_n, " ", set$taxlvl))) +
-  geom_col(color = "black") +
-  set$my_scale_fill + 
+  geom_col(color = "black", size = 0.1) +
+  scale_fill_viridis(discrete = TRUE, na.value = "grey")  +
   ylab(set$y_axis_label) +
   xlab(set$x_axis_label) +
   theme(strip.background = element_blank(),
+        legend.key.size = unit(0.9, "line"),
+        legend.text = element_text(margin = margin(0,10, 0, 1)),
         legend.position = "bottom")
 
 plots$ndvi_dot_plot <- ggplot(set$topntax_tbl, aes(fct_reorder(Alias, ndvi),
@@ -757,19 +769,18 @@ plots$shannon_dot_plot <- ggplot(set$topntax_tbl,
   ylab("Shannon")
 
 
-
-
 plots$combo_topn_custom <- ggarrange(plots$ndvi_dot_plot,
                                      plots$shannon_dot_plot,
                                      plots$topn_tax_custom,
                                      nrow = 3,
                                      heights = c(1, 1, 3),
-                                     align = "v")
+                                     align = "v") 
 
 save_plot(plots$combo_topn_custom, plot_name = paste0("Customized_NDVI_Shannon_plot"), 
-          filetype = tmp$out)
+          filetype = ".png")
+save_plot(plots$combo_topn_custom, plot_name = paste0("Customized_NDVI_Shannon_plot"), 
+          filetype = ".pdf")
 plots$combo_topn_custom
-
 ```
 
 

analysis/Nems/Nems_Analysis_pipeline_v4-3.Rmd

@@ -856,42 +856,69 @@ set$ps.topnTax <- cuphyr::abundant_tax_physeq(ps.trans, lvl = set$taxlvl,
                                               ignore_na = set$ignore_na)
 
 # Plot
-set$my_scale_fill <- my_scale_fill
+# Custom, more narrow color ranges based on viridis
+# Base order to have adjacent colors be distinct from each other
+sort_colors <- c(rbind(c(1:5), c(6:10), c(11:15), c(16:20)))
+# Customized color vectors
+n_col <- 20
+viridis_reds <- viridis(n_col, option = "B",
+begin = 0.7 ,end = 0.5)[sort_colors]
 
 
-set$topntax_tbl <- psmelt(set$ps.topnTax) %>% 
+set$topntax_tb <- psmelt(set$ps.topnTax) %>% 
                     as_tibble() %>%
                     left_join(set$alpha_div_ps_trans, by = "Sample") %>% 
-                    select(Genus, Alias, ndvi, ndvi_july, Abundance, Shannon) %>%
+                    select(Genus, Alias, ndvi, Abundance, Shannon) %>%
                     filter(Abundance > 0) %>%
-                    group_by(Genus, Alias, ndvi, ndvi_july, Shannon) %>%
+                    group_by(Genus, Alias, ndvi, Shannon) %>%
                     summarise(Abundance = sum(Abundance)) %>%
                     arrange(ndvi) %>%
                     mutate(ndvi_rank = c(1:length(ndvi))) 
                     
+set$other <- set$topntax_tb %>% 
+  group_by(Alias) %>% 
+  summarise(sumabu = sum(Abundance)) %>% 
+  mutate(Genus = 'Other', Abundance = 1-sumabu) %>% 
+  select(-sumabu)
+
+set$topntax_tbl <- bind_rows(set$topntax_tb, set$other) %>% 
+  mutate(Genus = factor(Genus, levels = c(
+    sort(unique(set$topntax_tb$Genus)),
+    "Other")
+    ))
+
+colors_comb <- c(
+  viridis(4, option = "D", begin = 0 ,end = 0.4),
+  viridis_reds[c(1,4)],
+  viridis(5, option = "D", begin = 0.5 ,end = 1)
+)
+names(colors_comb) <- levels(set$topntax_tbl$Genus)
+
+formatted_labs <- c(as.expression(lapply(levels(set$topntax_tbl$Genus)[1:10], 
+                                         function(x) bquote(italic(.(x))))),
+                    expression("Other"))
+
+set$my_scale_fill <- scale_fill_manual(values = colors_comb,
+                                       labels = formatted_labs,
+                                       na.value = "grey")
 
 plots$topn_tax_custom <- ggplot(set$topntax_tbl, aes(x = fct_reorder(Alias, ndvi),
                            y = Abundance,
                            fill = Genus)) + 
-                           #title = paste0("Top ", set$top_n, " ", set$taxlvl))) +
-  geom_col(color = "black") +
-  set$my_scale_fill + 
+  geom_col(color = "black", size = 0.1) +
+  set$my_scale_fill +
   ylab(set$y_axis_label) +
   xlab(set$x_axis_label) +
   theme(strip.background = element_blank(),
-        #strip.text = element_text(size = 12),
-        #axis.title=element_text(size=12),
-        #legend.text = element_text(size=12), 
+        legend.key.size = unit(0.9, "line"),
+        legend.text = element_text(margin = margin(0,10, 0, 1)),
         legend.position = "bottom")
 
 plots$ndvi_dot_plot <- ggplot(set$topntax_tbl, aes(fct_reorder(Alias, ndvi),
                            y = ndvi)) +
                              geom_point() +
     theme(strip.background = element_blank(),
-         # strip.text = element_text(size = 12),
-         # axis.title=element_text(size=12),
-         # legend.text = element_text(size=12),
-          axis.title.x=element_blank()) +
+        axis.title.x=element_blank()) +
   ylab("NDVI")
 
 plots$shannon_dot_plot <- ggplot(set$topntax_tbl, 
@@ -899,26 +926,23 @@ plots$shannon_dot_plot <- ggplot(set$topntax_tbl,
                            y = Shannon)) +
                              geom_point() +
     theme(strip.background = element_blank(),
-         # strip.text = element_text(size = 12),
-         # axis.title=element_text(size=12),
-         # legend.text = element_text(size=12),
-          axis.title.x=element_blank()) +
+        axis.title.x=element_blank()) +
   ylab("Shannon")
 
 
-
-
 plots$combo_topn_custom <- ggarrange(plots$ndvi_dot_plot,
                                      plots$shannon_dot_plot,
                                      plots$topn_tax_custom,
                                      nrow = 3,
                                      heights = c(1, 1, 3),
-                                     align = "v")
+                                     align = "v") 
 
+save_plot(plots$combo_topn_custom, plot_name = paste0("Customized_NDVI_Shannon_plot"), 
+          filetype = ".png")
+save_plot(plots$combo_topn_custom, plot_name = paste0("Customized_NDVI_Shannon_plot"), 
+          filetype = ".pdf")
 plots$combo_topn_custom
 
-save_plot(plots$combo_topn_custom, plot_name = paste0("Customized_NDVI_Shannon_plot"), 
-          filetype = tmp$out)
 ```