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diff --git a/workflows/Figure_assembly/Figure_assembly.R b/workflows/Figure_assembly/Figure_assembly.R
index 4b1537f498906da866641683ddfa3618672b956e..c2cded8441d58578e907a7b2e5936394dc3f865c 100644
--- a/workflows/Figure_assembly/Figure_assembly.R
+++ b/workflows/Figure_assembly/Figure_assembly.R
@@ -23,7 +23,7 @@ if (file.exists(out)) {
cor_net <- here("runs/correlation_network/")
rna_fig <- here("runs/RNA_figures/")
prot_fig <- here("runs/Prot_Figures/")
-met_fig <- here("runs/")
+met_fig <- here("runs/Met_whole/")
prim_fig <- here("runs/polar_G")
multi <- here("runs/multiomics_integration/")
study17 <- here("studies/canal-1_2017_GH/resources/")
@@ -43,6 +43,7 @@ rem_y <- theme(axis.text.y = element_blank())
x_ax_ang <- theme(axis.text.x = element_markdown(angle = 45, vjust = 0.5))
add_axis <- theme(axis.title.x = element_text(size = 6),
axis.title.y = element_text(size = 6))
+md_text <- theme(text = element_markdown(size = 8))
# plot_comb <- function(...){
# plot_grid(...,
# labels = "AUTO",
@@ -50,6 +51,21 @@ add_axis <- theme(axis.title.x = element_text(size = 6),
# label_fontfamily = "Arial")
# }
+#Current workaround while get legend is adapted to new ggplot version
+get_legend_35 <- function(plot) {
+ # return all legend candidates
+ legends <- get_plot_component(plot, "guide-box", return_all = TRUE)
+ # find non-zero legends
+ nonzero <- vapply(legends, \(x) !inherits(x, "zeroGrob"), TRUE)
+ idx <- which(nonzero)
+ # return first non-zero legend if exists, and otherwise first element (which will be a zeroGrob)
+ if (length(idx) > 0) {
+ return(legends[[idx[1]]])
+ } else {
+ return(legends[[1]])
+ }
+}
+
# Phenotype ---------------------------------------------------------------
@@ -433,21 +449,27 @@ ggsave(here(out, "Figure_7_letter.pdf"), f7_letter, width = 21.59, height = 27.9
# Metabolome --------------------------------------------------------------
-f8a <- read_rds(here(rds_source, "Heatmap_all_met.RDS"))
+f8a <- read_rds(here(met_fig, "Heatmap_all_met.RDS"))
f8a
-f8b <- read_rds(here(rds_source, "Combined_bubble_metabolites.RDS"))
+f8b <- read_rds(here(met_fig, "fruit_yield_sad_cor_rel.RDS")) + bot_leg
f8b
-f8c <- read_rds(here(rds_source, "asparagine_leaves.RDS")) + bot_leg
+f8c <- read_rds(here(met_fig, "Combined_bubble_metabolites.RDS"))
f8c
-f8r2 <- plot_grid(f8b, f8c, ncol = 2, labels = c("B", "C"), rel_widths = c(2,1), hjust = -0.3, label_size = 12)
+f8d <- read_rds(here(met_fig, "asparagine_leaves.RDS")) + bot_leg
+f8d
+
+f8r1 <- plot_grid(f8a, f8b, ncol = 2, labels = c("A", "B"), rel_widths = c(1,1), hjust = -0.3, label_size = 12)
-f8 <- plot_grid(f8a, f8r2, nrow = 2, labels = c("A",""), rel_heights = c(3,2), hjust = -0.3, label_size = 12)
+f8r2 <- plot_grid(f8c, f8d, ncol = 2, labels = c("C", "D"), rel_widths = c(2,1), hjust = -0.3, label_size = 12)
+
+f8 <- plot_grid(f8r1, f8r2, nrow = 2, labels = c("",""), rel_heights = c(5,3), hjust = -0.3, label_size = 12)
f8
ggsave(here(out, "Figure_8.pdf"), f8, dpi = 600, width = 16.8, height = 20, units = "cm")
+ggsave(here(out, "Figure_8.png"), f8, dpi = 600, width = 16.8, height = 20, units = "cm")
header <- ggplot() + geom_text(aes(x = 0, y = 0 ,label = "Figure 8"), size = 20) + theme_void()
header
@@ -531,7 +553,7 @@ f11c <- read_rds(here("runs/correlation_network/PS_assem_comp_pmds.RDS")) +
rem_leg
f11c
-f11bc_leg <- get_legend(f11c + bot_leg)
+f11bc_leg <- get_legend_35(plot = f11c + bot_leg)
#plot_comb(f11a, f11b)
f11ab <- plot_grid(f11a, f11b, rel_widths = c(1,1),
@@ -548,7 +570,7 @@ f11 <- plot_grid(f11ab, f11_c_with_leg, rel_heights = c(8.4, 11.5),
label_size = 8)
f11
-
+set.seed(1)
ggsave(filename = here(out, "Figure_11.pdf"),
plot = f11,
dpi = 600,
@@ -556,6 +578,14 @@ ggsave(filename = here(out, "Figure_11.pdf"),
width = 16.8,
units = "cm")
+set.seed(20)
+ggsave(filename = here(out, "Figure_11.png"),
+ plot = f11,
+ dpi = 600,
+ height = 19.9,
+ width = 16.8,
+ units = "cm")
+
header <- ggplot() + geom_text(aes(x = 0, y = 0 ,label = "Figure 11"), size = 20) + theme_void()
header
diff --git a/workflows/Met_whole/Met_whole.R b/workflows/Met_whole/Met_whole.R
index be4ff2132d616baba4388260955ca334a7c47b99..82b2c30de47d82681ed65607aa5a7af54556139b 100644
--- a/workflows/Met_whole/Met_whole.R
+++ b/workflows/Met_whole/Met_whole.R
@@ -1,4 +1,6 @@
-rm(list = ls())
+
+# Library -----------------------------------------------------------------
+
library(tidyverse)
library(ggpubr)
library(glue)
@@ -8,11 +10,15 @@ library(ggbeeswarm)
library(extrafont)
library(ggprism)
library(viridis)
+library(pheatmap)
+library(ComplexHeatmap)
+library(circlize)
library(car)
library(broom)
library(here)
library(ggrepel)
library(openxlsx)
+library(data.table)
# Directory setting -------------------------------------------------------
@@ -176,6 +182,7 @@ com_theme <- theme(axis.text.x = element_markdown(angle = 45, hjust = 1, size =
# Heatmap all----------------------------------------------------------------
library(pheatmap)
+library(ComplexHeatmap)
red_met_class <- read_csv(here(dat_in, "reduced_met_classes.csv")) %>%
select(-n)
@@ -233,7 +240,8 @@ annotation_col <- heat_base %>%
#mutate(group = as_factor(str_c(tissue, genotype, treatment, sep = "_"))) %>%
filter(!is.na(geno_tissue_label)) %>%
select(tissue, genotype = geno_label, geno_tissue_label) %>%
- as.data.frame()
+ as.data.frame() %>%
+ arrange(genotype)
rownames(annotation_col) <- annotation_col$geno_tissue_label
@@ -264,6 +272,8 @@ ann_colors = list(
"Other" = "#000000")
)
+pheatmap.all <- Heatmap(mat.heat_nom)
+
pheatmap.all <- pheatmap(mat.heat_nom,
colorRampPalette(c("#440154FF", "white", "#FDE725FF"))(21),
#cellwidth = 16,
@@ -280,19 +290,141 @@ pheatmap.all <- pheatmap(mat.heat_nom,
number_color = "black",
fontsize_number = 6,
fontsize = 6,
+ #legend_labels = gt_render(c("M82", "*canal-1*")),
annotation_colors = ann_colors,
+ labels_col = gt_render(colnames(mat.heat_nom))
#filename = str_c(str_replace_all(Sys.Date(),"^.{2}|-",""),
# "cmQTL_val_1_heatmap_rel_tissue_wt.jpg",
# sep = "_")
)
-dev.off()
+if(!dev.cur() == 1){
+ dev.off()
+}
+
+# convert to complexheatmap
-heat_all <- ggplotify::as.ggplot(pheatmap.all)
-saveRDS(heat_all, here(out, "Heatmap_all_met.RDS"))
+annotation_row <- heat_nom %>%
+ select(Compound_Class)
-ggsave(plot = heat_all,
- here(out, "Heatmap_all.jpg"),
+rownames(annotation_row) <- heat_nom$met
+
+annotation_row <- annotation_row %>%
+ as.matrix()
+
+cc_vec = c("Amino Acid or derivative" = "#0072B2",
+ "Carboxylic Acid" = "#D55E00",
+ "Carbohydrate or derivative" = "#CC79A7",
+ "Cinnamic Acid" = "#484E37",
+ "Dipeptide" = "#4AEE2F",
+ "Flavonoid (glycosides)" = "#BAD23A",
+ "Galactolipid" = "#EF000B",
+ "Phospholipid" = "#19605B",
+ "Steroidal Glycoalkaloids" = "#7A5DF0",
+ "Triacylglyceride" = "#6E3455",
+ "Other" = "#000000")
+
+
+
+annotation_col <- heat_base %>%
+ distinct(tissue, treatment, geno_label, geno_tissue_label) %>%
+ #mutate(group = as_factor(str_c(tissue, genotype, treatment, sep = "_"))) %>%
+ filter(!is.na(geno_tissue_label)) %>%
+ select(tissue, genotype = geno_label, geno_tissue_label) %>%
+ mutate(genotype = as_factor(genotype),
+ tissue = as_factor(tissue),
+ genotype = fct_relevel(genotype, c("M82", "*canal-1*")),
+ tissue = fct_relevel(tissue, c("greenleaf", "whiteleaf", "stem"))) %>%
+ as.data.frame() %>%
+ arrange(genotype)
+
+rownames(annotation_col) <- annotation_col$geno_tissue_label
+
+annotation_col <- annotation_col %>%
+ select(-geno_tissue_label, tissue, genotype)
+
+heat_cols <- colnames(mat.heat_nom)
+
+annotation_col <- annotation_col[match(colnames(mat.heat_nom), rownames(annotation_col)),]
+
+col_fun <- colorRamp2(seq(-5, 5, length = 3), c("blue", "white", "red"))
+
+column_ha <- HeatmapAnnotation(df = annotation_col,
+ annotation_name_side = "left",
+ col = list(
+ genotype = c("*canal-1*" = "orange",
+ "M82" = "blue"),
+ tissue = c("greenleaf" = "darkgreen",
+ "whiteleaf" = "beige",
+ "stem" = "lightgreen")
+ ),
+ annotation_legend_param = list(
+ genotype = list(#nrow = 1,
+ labels = gt_render(c("M82", "*canal-1*")),
+ labels_gp = gpar(fontsize = 6),
+ title_gp = gpar(fontsize = 8)),
+ tissue = list(#nrow = 1,
+ labels_gp = gpar(fontsize = 6),
+ title_gp = gpar(fontsize = 8))
+ ),
+ annotation_name_gp = gpar(fontsize = 8)
+)
+
+heat_map <- Heatmap(mat.heat_nom,
+ width = unit(3, "cm"),
+ cluster_rows = T,
+ cluster_columns = T,
+ name = "Matrix",
+ col = col_fun,
+ #column_labels = gt_render(colnames(met_yield_sad_cor)),
+ heatmap_legend_param = list(title_gp = gpar(fontsize = 8),
+ number_gp = gpar(fontsize = 6),
+ labels_gp = gpar(fontsize = 6)),
+ #row_split = annotation_row$Compound_Class,
+ top_annotation = column_ha,
+ #left_annotation = row_ha,
+ row_names_gp = gpar(fontsize = 6),
+ column_names_gp = gpar(fontsize = 8),
+ column_dend_height = unit(5, "mm"),
+ row_dend_width = unit(5, "mm"),
+ show_row_names = F,
+ show_column_names = T,
+ column_labels = gt_render(colnames(mat.heat_nom)),
+ row_title = NULL
+)
+
+heat_map
+
+anno_row_ht <- Heatmap(annotation_row,
+ width = unit(3, "mm"),
+ col = cc_vec,
+ name = "Compound Class" ,
+ show_row_names = F,
+ heatmap_legend_param = list(title_gp = gpar(fontsize = 8),
+ number_gp = gpar(fontsize = 6),
+ labels_gp = gpar(fontsize = 6)),
+ column_labels = "")
+
+anno_row_ht
+
+heat_comp <- draw(heat_map + anno_row_ht,
+ main_heatmap = "Matrix",
+ heatmap_legend_side = "left",
+ annotation_legend_side = "left")
+
+heat_grid <- grid.grabExpr(draw(heat_map + anno_row_ht,
+ main_heatmap = "Matrix",merge_legend = T,
+ heatmap_legend_side = "left",
+ annotation_legend_side = "left"))
+
+heat_gg <- ggplotify::as.ggplot(heat_grid)
+
+heat_gg
+
+saveRDS(heat_gg, here(out, "Heatmap_all_met.RDS"))
+
+ggsave(plot = heat_gg,
+ here(out, "Heatmap_all_met.jpg"),
width = 16,
height = 10,
units = "cm",
@@ -721,12 +853,8 @@ saveRDS(last_plot(), here(out,
ggsave(here(out, str_c("Bubble_", "comb", ".png")),
width = 16.5, height = 10, units = "cm")
-
-
# Heatmap SAD----------------------------------------------------------------
-library(pheatmap)
-
plot_label <- read.xlsx("studies/canal-1_2017_GH/resources/Labels.xlsx")
red_met_class <- read_csv(here(dat_in, "reduced_met_classes.csv")) %>%
@@ -862,10 +990,12 @@ pheatmap.all <- pheatmap(mat.heat_nom,
# sep = "_")
)
-dev.off()
-
+if(!dev.cur() == 1){
+ dev.off()
+}
heat_all <- ggplotify::as.ggplot(pheatmap.all)
-saveRDS(heat_all, here(out, "Heatmap_all_met.RDS"))
+heat_all
+saveRDS(heat_all, here(out, "Heatmap_all_met_fruit.RDS"))
ggsave(plot = heat_all,
here(out, "Heatmap_fruit_sad.jpg"),
@@ -887,18 +1017,23 @@ isa_fruit <- isa_tidy %>%
filter(!str_detect(genotype, "on"), ! year == 2017) %>%
distinct(source_name_study, genotype, genotype_alt, treatment)
-yield_sad <- yield %>%
+yield_tidy <- yield %>%
filter(fruit_yield != 0) %>%
mutate(aliquot_ID = as.character(aliquot_ID)) %>%
left_join(isa_fruit, by = c("aliquot_ID" = "source_name_study",
- "treatment")) %>%
+ "treatment"))
+fruit_met_tidy <- fc_1_ind %>%
+ filter(!str_detect(genotype, "on"),
+ treatment == "control", tissue == "fruit") %>%
+ mutate(genotype = as_factor(genotype))
+
+yield_sad <- yield_tidy %>%
+ filter(aliquot_ID %in% fruit_met_tidy$aliquot_ID) %>%
group_by(treatment, genotype, genotype_alt) %>%
mutate(yield_sad = (abs(fruit_yield - median(fruit_yield))/median(fruit_yield)))
-fruit_met_sad <- fc_1_ind %>%
- filter(!str_detect(genotype, "on"),
- treatment == "control", tissue == "fruit") %>%
- mutate(genotype = as_factor(genotype)) %>%
+fruit_met_sad <- fruit_met_tidy %>%
+ filter(aliquot_ID %in% yield_tidy$aliquot_ID) %>%
group_by(tissue, treatment, genotype, met) %>%
mutate(sad = (abs(fc - median(fc)))/median(fc)) %>%
ungroup()
@@ -908,53 +1043,267 @@ fruit_met_sad_wide <- fruit_met_sad %>%
names_from = met,
values_from = sad)
-# Test metabolite variation -----------------------------------------------
+fruit_all_sad <- fruit_met_sad_wide %>%
+ left_join(yield_sad) %>%
+ #filter(genotype == "CANA1") %>%
+ select(-fruit_yield)
+
+cor_mat <- fruit_all_sad %>%
+ select(where(is.numeric)) %>%
+ as.matrix()
+
+met_yield_sad_cor <- cor(cor_mat, method = "spearman")
+
+#heatmap(met_yield_sad_cor)
+
+
+## Correlation heatmap -----------------------------------------------------
+
+#Classes by platform
+
+prim <- here("runs/polar_GC_analysis/")
+sec <- here("runs/polar_LC_analysis")
+lip <- here("runs/apolar_LC_analysis")
+
+prim_tib <- fread(here(prim, "Prim_wide.csv"))
+sec_tib <- fread(here(sec, "Sec_wide.csv"))
+lip_tib <- fread(here(lip, "Lip_wide.csv"))
+
+prim_nodes <- prim_tib %>%
+ select(-sample_name_unique) %>%
+ colnames() %>%
+ as_tibble() %>%
+ mutate(class = "prim met",
+ lvl = 3)
+
+sec_nodes <- sec_tib %>%
+ select(-sample_name_unique) %>%
+ colnames() %>%
+ as_tibble() %>%
+ mutate(class = "sec met",
+ lvl = 3)
+
+lip_nodes <- lip_tib %>%
+ select(-sample_name_unique) %>%
+ colnames() %>%
+ as_tibble() %>%
+ mutate(class = "lip met",
+ lvl = 3)
+
+all_nodes <- prim_nodes %>%
+ bind_rows(sec_nodes) %>%
+ bind_rows(lip_nodes) %>%
+ rename(met = value) %>%
+ mutate(Trait_Class = as_factor(class)) %>%
+ add_row(met = "yield_sad", Trait_Class = "yield") %>%
+ mutate(identity = as_factor(if_else(Trait_Class == "yield", "yield", "metabolite")),
+ Trait_Class = fct_relevel(Trait_Class, c("prim met", "sec met", "lip met", "yield")))
+
+annotation_col <- all_nodes %>%
+ filter(!is.na(met)) %>%
+ as.data.frame()
+
+# annotation_col <- met_dat %>%
+# left_join(red_met_class) %>%
+# select(-Compound_Name, -Compound_Class) %>%
+# rename(Trait_Class = Compound_Class_dense) %>%
+# add_row(met = "yield_sad", Trait_Class = "yield") %>%
+# as.data.frame()
+
+rownames(annotation_col) <- annotation_col$met
+rownames(annotation_col) <- annotation_col$met
+
+annotation_col <- annotation_col[match(rownames(met_yield_sad_cor), rownames(annotation_col)),]
+
+annotation_col <- annotation_col %>%
+ select(-met, -class, - lvl)
+
+annotation_row <- annotation_col
+
+col_fun <- colorRamp2(seq(-1, 1, length = 3), c("purple", "white", "yellow"))
+
+column_ha <- HeatmapAnnotation(df = annotation_col,
+ annotation_name_side = "left",
+ col = list(
+ Trait_Class = c("prim met" = cb_scale[5],
+ "sec met" = cb_scale[6],
+ "lip met" = cb_scale[7],
+ "yield" = "gold")
+ ,
+ identity = c("yield" = cb_scale[2],
+ "metabolite" = cb_scale[8])
+ ),
+ annotation_legend_param = list(
+ Trait_Class = list(nrow = 2,
+ labels_gp = gpar(fontsize = 7),
+ title_gp = gpar(fontsize = 8))
+ ,
+ identity = list(labels_gp = gpar(fontsize = 7),
+ title_gp = gpar(fontsize = 8))
+ ),
+ annotation_name_gp = gpar(fontsize = 8)
+)
+
+heat_map1 <- Heatmap(met_yield_sad_cor,
+ cluster_rows = T,
+ cluster_columns = T,
+ name = "Correlation",
+ col = col_fun,
+ #column_labels = gt_render(colnames(met_yield_sad_cor)),
+ heatmap_legend_param = list(direction = "horizontal",
+ title_gp = gpar(fontsize = 8),
+ number_gp = gpar(fontsize = 6),
+ labels_gp = gpar(fontsize = 7)),
+ #row_split = annotation_row$Compound_Class,
+ bottom_annotation = column_ha,
+ #left_annotation = row_ha,
+ row_names_gp = gpar(fontsize = 6),
+ column_names_gp = gpar(fontsize = 8),
+ show_row_names = F,
+ show_column_names = F,
+ row_title = NULL
+)
+
+heat_map1
+
+heat_cor <- grid.grabExpr(draw(heat_map1, annotation_legend_side = "bottom"))
+heat_cor
+
+heat_gg <- ggplotify::as.ggplot(heat_cor)
+
+heat_gg
+
+saveRDS(heat_gg,
+ here(out, "fruit_yield_sad_cor.RDS"))
+
+ggsave(here(out, "fruit_yield_sad_cor.jpg"),
+ width = 16.8,
+ height = 19.9,
+ units = "cm")
+
+fruit_all_sad %>%
+ ggplot(aes(x = yield_sad, y = m_11, color = genotype)) +
+ geom_point()
+
+# Heatmap relative to wildtype -----------------------------------------------
library(rstatix)
-sad <- fc_1_ind %>%
- filter(!str_detect(genotype, "on"),
- treatment == "control", tissue == "fruit") %>%
- mutate(genotype = as_factor(genotype)) %>%
- group_by(tissue, treatment, genotype, met) %>%
- mutate(sad = (abs(fc - median(fc)))/median(fc)) %>%
- ungroup()
+sad <- fruit_all_sad %>%
+ pivot_longer(cols = where(is.numeric),
+ names_to = "met",
+ values_to = "sad")
-signif <- sad %>%
+sad_M82 <- sad %>%
+ filter(genotype == "M82") %>%
group_by(tissue, treatment, met) %>%
- wilcox_test(formula = sad ~ genotype,
- ref.group = "M82",
- p.adjust.method = "fdr")
-
-p1 <- sad %>%
- filter(met == "m_86", str_detect(tissue, "fruit"), treatment == "control", !str_detect(genotype, "on")) %>%
- #mutate(genotype = as_factor(geno_tissue_label),
- # genotype = fct_relevel(genotype, c("gl M82", "gl *canal-1*", "wl *canal-1*"))) %>%
- ggplot(aes(x = genotype, y = sad)) +
- geom_boxplot() +
- geom_dotplot()#+
- #geom_errorbar(aes(ymin = (mean_fc-se), ymax = (mean_fc + se)), position = position_dodge(0.9), width = 0.25, linewidth = 0.75)+
- stat_pvalue_manual(step.group.by = c("treatment", "tissue_group"), sig_comb_bar, label = "p.signif", y.position = "y.position",
- step.increase = 0.07, tip.length = 0.01,
- hide.ns = F) +
- # theme(axis.text.x = element_markdown(angle = 45, hjust = 1),
- # panel.background = element_rect(fill = "white"),
- # panel.border = element_rect(color = "black",fill = NA),
- # text = element_text(size = 14),
- # legend.title = element_blank(),
- # legend.text = element_markdown()) +
- com_theme +
- xlab("") +
- ylab("Mean fold-change") +
- #facet_grid(rows = vars(treatment), cols = vars(tissue_group)) +
- ggtitle(label = "asparagine") +
- scale_fill_manual(values = c("darkgreen", "beige"), aesthetics = "fill") +
- scale_y_log10()
+ summarise(M82_sad = mean(sad))
-p1
+sad_fc <- sad %>%
+ group_by(tissue, treatment, genotype, met) %>%
+ summarise(mean_sad = mean(sad)) %>%
+ left_join(sad_M82) %>%
+ mutate(mean_fc = mean_sad/M82_sad)
-ggsave(plot = p1, here(out, "asparagine.png"),
- width = 16, height = 10, units = "cm")
+sad_fc_mut <- sad_fc %>%
+ filter(genotype == "CANA1") %>%
+ left_join(plot_label, by = c("genotype" = "geno_old",
+ "tissue" = "tissue_label"))
+heat_nom <- sad_fc_mut %>%
+ group_by(met) %>%
+ mutate(log_norm = log2(mean_fc),
+ log_norm = if_else(is.infinite(log_norm), 0, log_norm),
+ log_norm_level = (log_norm - mean(log_norm))/(max(log_norm)-min(log_norm)),
+ z_score = (mean_fc - mean(mean_fc))/(max(mean_fc)-min(mean_fc))) %>%
+ ungroup() %>%
+ pivot_wider(id_cols = c(met),
+ names_from = geno_tissue_label,
+ values_from = log_norm) %>%
+ left_join(all_nodes) %>%
+ as.data.frame()
+rownames(heat_nom) <- heat_nom$met
-saveRDS(p1, here(out, "asparagine_leaves.RDS"))
+heat_nom <- heat_nom[match(rownames(met_yield_sad_cor), rownames(heat_nom)),]
+
+mat.heat_nom <- heat_nom %>%
+ select(contains("fr")) %>% as.matrix()
+
+annotation_row <- all_nodes %>%
+ filter(!is.na(met)) %>%
+ as.data.frame()
+
+rownames(annotation_row) <- annotation_row$met
+
+annotation_row <- annotation_row[match(rownames(mat.heat_nom), rownames(annotation_row)),]
+
+annotation_row <- annotation_row %>%
+ select(-met, -class, - lvl)
+
+col_fun <- colorRamp2(seq(-3, 3, length = 3), c("blue", "white", "red"))
+
+# row_ha <- rowAnnotation(df = annotation_row,
+# anno_block())
+# ,
+# col = list(
+# Trait_Class = c("prim met" = cb_scale[5],
+# "sec met" = cb_scale[6],
+# "lip met" = cb_scale[7],
+# "yield" = "gold")
+# #,
+# # identity = c("SCO2" = cb_scale[2],
+# # "other" = cb_scale[8])
+# ),
+# annotation_legend_param = list(
+# Trait_Class = list(labels_gp = gpar(fontsize = 8),
+# title_gp = gpar(fontsize = 10))
+# #,
+# # identity = list(labels_gp = gpar(fontsize = 8),
+# # title_gp = gpar(fontsize = 10))
+# ),
+# annotation_name_gp = gpar(fontsize = 8)
+# )
+
+heat_map2 <- Heatmap(mat.heat_nom,
+ cluster_rows = T,
+ cluster_columns = T,
+ width = unit(5, "mm"),
+ name = "LFC rel WT",
+ col = col_fun,
+ #column_labels = gt_render(colnames(met_yield_sad_cor)),
+ heatmap_legend_param = list(direction = "horizontal",
+ title_gp = gpar(fontsize = 8),
+ number_gp = gpar(fontsize = 6),
+ labels_gp = gpar(fontsize = 7)),
+ #row_split = annotation_row$Compound_Class,
+ #top_annotation = column_ha,
+ #left_annotation = row_ha,
+ row_names_gp = gpar(fontsize = 6),
+ column_names_gp = gpar(fontsize = 8),
+ show_row_names = F,
+ show_column_names = F,
+ row_title = NULL
+)
+
+heat_map2
+
+combined <- heat_map1 + heat_map2
+
+#heat_map <- draw(test, main_heatmap = "Matrix", annotation_legend_side = "bottom")
+
+heat_map <- grid.grabExpr(draw(combined,
+ main_heatmap = "Correlation",
+ annotation_legend_side = "bottom",
+ heatmap_legend_side = "bottom"))
+
+heat_gg <- ggplotify::as.ggplot(heat_map)
+
+heat_gg
+
+saveRDS(heat_gg,
+ here(out, "fruit_yield_sad_cor_rel.RDS"))
+
+ggsave(here(out, "fruit_yield_sad_cor_rel.jpg"),
+ width = 16.8,
+ height = 17.9,
+ units = "cm")
diff --git a/workflows/correlation_network/correlation_network.R b/workflows/correlation_network/correlation_network.R
index 3356e5b96edef01bb10328cac931116d55ff45d2..24839a96de782438f3336d02dca98bb1cd481e49 100644
--- a/workflows/correlation_network/correlation_network.R
+++ b/workflows/correlation_network/correlation_network.R
@@ -369,8 +369,15 @@ ggraph(sco2_neigh, layout = "focus", focus = sco2_in_sco2_neigh) +
draw_circle(max.circle = 1) +
geom_edge_link(aes(color = as_factor(Correlation))) +
geom_node_point(aes(fill = as_factor(class)), shape = 21, size = 3, stroke = 0.05) +
- geom_node_label(aes(label = name), repel = T, size = 6/.pt, force = 2,
- force_pull = 0.1, min.segment.length = 0, max.overlaps = 200) +
+ geom_node_label(aes(label = name),
+ label.padding = unit(0.1, "lines"),
+ label.size = 0.1,
+ repel = T,
+ size = 6/.pt,
+ force = 20,
+ force_pull = 0.1,
+ min.segment.length = 0,
+ max.overlaps = 200) +
theme_blank() +
scale_fill_manual(values = cb_scale[3:7], aesthetics = "fill") +
scale_edge_color_manual(values = c(cb_scale[2], cb_scale[1])) +
diff --git a/workflows/multiomics_integration/multiomics_integration.R b/workflows/multiomics_integration/multiomics_integration.R
index bd9ae3bbfd7046b2ce9b2d0f6973b578f0c94db0..e09d4d5dd60bcb5a224994b1149f0f3dd66a70af 100644
--- a/workflows/multiomics_integration/multiomics_integration.R
+++ b/workflows/multiomics_integration/multiomics_integration.R
@@ -27,7 +27,7 @@ dat_in <- here("assays/canal-1_polar_GC_MS_2017/dataset/")
file.copy(from = here("assays/canal-1_polar_GC_MS_2017/dataset/Metabolism.sbgn"),
to = here(out, "Metabolism.sbgn"))
-file.copy(from = here("assays/canal-1_polar_GC_MS_2017/dataset/Multilevel_Metabolism.sbgn"),
+file.copy(from = here("assays/canal-1_polar_GC_MS_2017/dataset/Multilevel_Metabolism_safe1_newt.sbgn"),
to = here(out, "Multilevel_Metabolism.sbgn"), overwrite = T)
file.copy(from = here("assays/canal-1_polar_GC_MS_2017/dataset/Metabolism_pathways.sbgn"),