Create a heatmap of select features or a choice pathway.

Create a heatmap for user-specified features for a given tissue and ome combination. This function replaces plot_pathway_features

Usage

plot_feature_heatmap(
  feature_ids = NULL,
  set_id = NULL,
  platforms = NULL,
  selected_tissue = c("adipose", "blood", "muscle"),
  selected_ome = c("transcript-rna-seq", "prot-pr", "prot-ph", "metab", "prot-ol"),
  contrast_type = "exercise_with_controls",
  column_title = "",
  filename,
  max_size = NULL,
  post_min = NULL,
  post_hr = NULL,
  full_modality_names = FALSE,
  multi_tissue_clust_rows = FALSE,
  right_annotation = NULL,
  heatmap_args = list(),
  draw_args = list(),
  return_drawing = FALSE,
  verbose = TRUE,
  ...
)

Arguments

feature_ids

character or NULL; vector of feature IDs that will appear in the heatmap. Must be a subset of HUMAN_FEATURE_TO_ID[["feature_id"]].

set_id

character of NULL; if not NULL, the feature IDs in the set will be used to filter rows for the heatmap, but those IDs will not be used for the heatmap row labels.

platforms

character or NULL; the platform(s) used to filter metabolites. If NULL (default), metabolites in feature_ids will be selected from all available platforms. If metabolites appear in more than one platform, the platform will appear before the metabolite name in the row names of the heatmap.

selected_tissue

character; the tissue that will be used to create the heatmap.

selected_ome

character; the ome that will be used to create the heatmap.

contrast_type

character; the type of contrasts to plot. One of "exercise_with_controls" (default), "exercise_no_controls", "Endur_vs_Resist", "baseline", or "control_only".

column_title

character; the title you'd like to include for the columns. Usually empty

filename

character; optional file name used to save the heatmap. If provided, the heatmap will not be drawn. Ignored when return_drawing = TRUE.

max_size

numeric; largest number of pathways to display, if a pathway has too many features. Will automatically chose the first n pathways.

post_min

numeric; for experiments, timepoints could be either 15, 30, or 45 minutes depending on the analysis, this argument allows users to specify which of those 3 values to use, by default the value is NULL and will provide a generic label of post 15/30/45 min

post_hr

numeric; for experiments, timepoints could be either 3.5 or 4 hours depending on the analysis, this argument allows users to specify which of those 2 values to use, by default the value is NULL and will provide a generic label of post 3.5/4 hr

full_modality_names

logical; if TRUE the modality values are set as Endurance Exercise and Resistance Exercise but if FALSE the modality values are set as EE and RE (by default the value is FALSE)

multi_tissue_clust_rows

logical; whether to cluster rows when more than one tissue is selected. Rows are restricted to features with a value in every column, since missing values break row clustering. Single-tissue heatmaps are always clustered.

right_annotation

NULL, a HeatmapAnnotation, or a function. A function receives the row labels in heatmap row order and must return a row HeatmapAnnotation; use it when the annotation depends on which feature each row is. A HeatmapAnnotation is used as is and must already be in row order.

heatmap_args

list; arguments passed to Heatmap. They override the defaults set here, e.g. list(cluster_rows = FALSE).

draw_args

list; arguments passed to draw. They override the defaults set here, e.g. list(newpage = FALSE).

return_drawing

logical; if TRUE, nothing is drawn or saved. Instead a list is returned so the caller controls the graphics device.

verbose

logical; for specific warnings and additional information.

...

Additional parameters to be added to a ComplexHeatmap call

Value

If return_drawing = FALSE (default), nothing; the heatmap is drawn on the current device, or saved to filename if provided. If return_drawing = TRUE, a list with components draw, a function with no arguments that draws the heatmap on the current device without starting a new page, and width and height, the suggested page size in inches.

Author

Tyler Sagendorf, Damon Leach, Christopher Jin

Examples

if (FALSE) { # \dontrun{
plot_feature_heatmap(set_id = "11725",
  DA_list = DA_list,
  contrast_type = "exercise_with_controls",
  selected_tissue = "muscle",
  selected_ome = "prot-ph",
  filename = "sandbox/test_feature_heatmap.pdf")

# Draw on a device the caller opens, with a row annotation
hm <- plot_feature_heatmap(
  feature_ids = c("ENSG00000109819.9", "ENSG00000112715.26",
                  "ENSG00000119508.18", "ENSG00000162772.17"),
  selected_tissue = c("muscle", "adipose"),
  selected_ome = "transcript-rna-seq",
  multi_tissue_clust_rows = TRUE,
  right_annotation = function(row_labels) {
    ComplexHeatmap::rowAnnotation(group = rep("A", length(row_labels)))
  },
  return_drawing = TRUE)
grDevices::pdf("heatmap.pdf", width = hm$width, height = hm$height)
hm$draw()
grDevices::dev.off()
} # }