Heatmap of total triacylglycerol concentrations

This article generates a heatmap of total TAG concentrations (Fig. 5E).

library(MotrpacRatTraining6moWATData)
library(ComplexHeatmap)
library(dplyr)
library(Biobase)

save_plots <- dir.exists(paths = file.path("..", "..", "plots"))

# Scaling factor for plot elements
scale <- 2

# Barplot annotation
TG_hm <- HeatmapAnnotation(`Median \nTotal TAG \n(ug/mg tissue)` =
                             anno_barplot(METAB_TG_CONC$median_total_TG,
                                          bar_width = 1, # 0.85
                                          height = unit(45 * scale, "pt")),
                           annotation_name_gp = gpar(fontsize = 7 * scale))

# Column annotation
ha <- select(pData(METAB_TG_CONC), sex, timepoint) %>%
  transmute(Sex = sex,
            Timepoint = timepoint) %>%
  HeatmapAnnotation(
    df = .,
    border = TRUE,
    gp = gpar(col = "black"),
    gap = 0,
    which = "column",
    height = unit(6 * 2, "pt") * scale,
    col = list(
      Sex = c("Female" = "#ff6eff",
              "Male" = "#5555ff"),
      Timepoint = c("SED" = "white",
                    "1W" = "#F7FCB9",
                    "2W" = "#ADDD8E",
                    "4W" = "#238443",
                    "8W" = "#002612")
    ),
    annotation_name_gp = gpar(fontsize = 7 * scale),
    annotation_legend_param = list(Timepoint = list(
      at = c("SED", "1W", "2W", "4W", "8W")),
      border = "black",
      labels_gp = gpar(fontsize = 6.5 * scale),
      title_gp = gpar(fontsize = 7 * scale, fontface = "bold")
    )
  )

# Subset to top 20 metabolites
METAB_TG_CONC <- METAB_TG_CONC[order(fData(METAB_TG_CONC)[["rank"]]), ][1:20, ]

ht <- exprs(METAB_TG_CONC) %>%
  Heatmap(matrix = .,
          col = circlize::colorRamp2(
            breaks = c(-1.9, 0, 2.1),
            colors = c("#3366ff", "white", "darkred")
          ),
          cluster_columns = FALSE,
          cluster_rows = FALSE,
          show_column_names = FALSE,
          row_labels = fData(METAB_TG_CONC)[["name_in_figures"]],
          top_annotation = ha,
          border = "black",
          row_names_gp = gpar(fontsize = 5 * scale),
          height = nrow(.) * unit(5.5, "pt") * scale,
          width = ncol(.) * unit(5.5, "pt") * scale,
          column_split = rep(1:2, each = 5),
          column_title = NULL,
          heatmap_legend_param = list(
            title = "Standardized\nMedian\nConcentration",
            at = c(-1.9, -1:1, 2.1),
            title_gp = gpar(fontsize = 7 * scale,
                            fontface = "bold"),
            labels_gp = gpar(fontsize = 6 * scale),
            legend_height = 5 * scale * unit(8, "pt"),
            border = "black"
          ))

# Stack barplot on top of heatmap
ht <- TG_hm %v% ht

# Save
pdf(file = file.path("..", "..", "plots", "total_TAG_heatmap.pdf"),
    width = 2.5 * scale, height = 2.5 * scale, family = "ArialMT")
draw(ht, merge_legends = TRUE,
     align_heatmap_legend = "heatmap_top",
     align_annotation_legend = "heatmap_top")
dev.off()

Tyler Sagendorf

01 May, 2024