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Create a heatmap of select features or a choice pathway.

plot_feature_heatmap.Rd

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,
  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.

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; if you'd like to cluster rows specifically in a multi-tissue case

verbose

logical; for specific warnings and additional information.

...

Additional parameters to be added to a ComplexHeatmap call

Value

Nothing. A heatmap is drawn or saved to a file if filename is provided.

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")
} # }