Create a bubble heatmap of molecular signatures from CAMERA-PR or PTM-SEA results — plot_enrich_heatmap • MotrpacHumanPreSuspensionAnalysis

Create a heatmap of molecular signatures for a given tissue, ome, and contrast type combination from CAMERA-PR results (CAMERA_RESULTS or the output of run_cameraPR()) or PTM-SEA results (PTMSEA_RESULTS).

Usage

plot_enrich_heatmap(
  x,
  set_ids = NULL,
  selected_tissues = c("adipose", "blood", "muscle"),
  selected_ome = c("transcript-rna-seq", "prot-pr", "prot-ph", "metab", "prot-ol"),
  contrast_type = c("exercise_with_controls", "exercise_no_controls", "Endur_vs_Resist",
    "baseline", "control_only"),
  padj_cutoff = 0.05,
  n_top = 6L,
  zscore_colors = c("#3366ff", "darkred"),
  filename = NULL,
  return_drawing = FALSE
)

Arguments

x: a data.frame of CAMERA-PR results with a z.std column, such as CAMERA_RESULTS or the output of run_cameraPR(), or PTM-SEA results with an NES column, such as PTMSEA_RESULTS.
set_ids: character or NULL; one or more of x$set_id. The dataset x will be filtered to these sets. If NULL, the top 6 most significant sets from each contrast will be selected.
selected_tissues: character; one or more tissues that will be used to create the heatmap. If multiple tissues are selected, only those terms tested in at least two tissues will be plotted.
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".
padj_cutoff: numeric; the p-value cutoff to add an asterisk indicating statistical significance.
n_top: integer; if set_ids is NULL, the n_top most significant molecular signatures from each tissue and contrast will be selected.
zscore_colors: character; length 2 vector of colors for the smallest and largest z-scores. Default is "#3366ff" (blue) and "darkred".
filename: character; path to a PDF file to save the heatmap. Ignored if return_drawing = TRUE.
return_drawing: logical; if TRUE, nothing is drawn or saved. Instead a list is returned so the caller controls the graphics device.

Value

If return_drawing = FALSE (default), nothing; the heatmap is saved to filename. 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; width and height, the suggested page size in inches; and n_sets, the number of sets drawn.

Author

Tyler Sagendorf