Revised top n genera figures for all markers

Revision request, reknitted as a result

analysis/16S/16S_Analysis_pipeline_v4-3.Rmd

@@ -817,9 +817,9 @@ set$ignore_na = TRUE
 ##### Optional settings (sensible defaults) #####
 
 # Can be changed to change the width (in cm) of the saved plot.
-set$wp = 20
+set$wp = 25
 # Can be changed to change the height (in cm) of the saved plot.
-set$hp = 13
+set$hp = 15
 # Can be changed to change the resolution (in dpi) of the saved plot.
 set$res = 300
 
@@ -843,7 +843,7 @@ 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$alpha_div_ps_trans, by = "Sample") %>% 
                     select(Genus, Alias, ndvi, Abundance, Shannon) %>%
@@ -853,35 +853,34 @@ set$topntax_tbl <- psmelt(set$ps.topnTax) %>%
                     arrange(ndvi) %>%
                     mutate(ndvi_rank = c(1:length(ndvi))) 
                     
-set$other <- set$topntax_tbl %>% 
+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_tbl, set$other)
+set$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") +
+  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(),
-        # strip.text = element_text(size = 16),
-       # axis.title=element_text(size=16),
-       # legend.text = element_text(size=14), 
+        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 = 16),
-        # axis.title=element_text(size=16),
-       # legend.text = element_text(size=14)
         axis.title.x=element_blank()) +
   ylab("NDVI")
 
@@ -890,9 +889,6 @@ plots$shannon_dot_plot <- ggplot(set$topntax_tbl,
                            y = Shannon)) +
                              geom_point() +
     theme(strip.background = element_blank(),
-          #strip.text = element_text(size = 16),
-        #axis.title=element_text(size=16),
-        #legend.text = element_text(size=14),
         axis.title.x=element_blank()) +
   ylab("Shannon")
 
@@ -905,7 +901,9 @@ plots$combo_topn_custom <- ggarrange(plots$ndvi_dot_plot,
                                      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/FITS1/FITS1_Analysis_pipeline_v4-3.Rmd

@@ -726,7 +726,7 @@ 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$alpha_div_ps_trans, by = "Sample") %>% 
                     select(Genus, Alias, ndvi, Abundance, Shannon) %>%
@@ -736,17 +736,28 @@ set$topntax_tbl <- psmelt(set$ps.topnTax) %>%
                     arrange(ndvi) %>%
                     mutate(ndvi_rank = c(1:length(ndvi))) 
                     
-
-plots$topn_tax_custom <- ggplot(set$topntax_tbl, aes(
-  x = fct_reorder(Alias, 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),
@@ -765,17 +776,17 @@ 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
 
 ```