deedee_heatmap: DeeDee Heatmap

In lea-rothoerl/DeeDee: Comparative Evaluation and Visualization of Differential Expression Analyses

Description

deedee_heatmap creates a heatmap depicting the logFC as a measure of the differential expression of the first genes in the given datasets.

Usage

deedee_heatmap(
  data,
  show_first = 25,
  show_gene_names = FALSE,
  dist = "euclidean",
  clust = "average",
  show_na = FALSE,
  pthresh = 0.05
)

Arguments

data	named list of results from deedee_prepare()
show_first	indicating the number of genes depicted (default = 25)
show_gene_names	boolean, show row names next to heatmap (default = FALSE)
dist	select the distance measure (euclidean, manhattan, pearson, spearman)
clust	select the clustering method (single, complete, average, centroid)
show_na	boolean, include genes with NA values in heatmap (default = FALSE)
pthresh	threshold for p-values to be in-/excluded (default = 0.05)

Value

Heatmap object (plottable with show()/print()). The resulting heatmap (res) can be opened in a Shiny App with interactive functionality by running the command ht_shiny(res) (see package InteractiveComplexHeatmap).

Examples

data(DE_results_IFNg_naive, package = "DeeDee")
IFNg_naive <- deedee_prepare(IFNg_naive, "DESeq2")

data(DE_results_IFNg_both, package = "DeeDee")
IFNg_both <- deedee_prepare(IFNg_both, "DESeq2")

data(DE_results_Salm_naive, package = "DeeDee")
Salm_naive <- deedee_prepare(Salm_naive, "DESeq2")

data(DE_results_Salm_both, package = "DeeDee")
Salm_both <- deedee_prepare(Salm_both, "DESeq2")

dd_list <- list(
  IFNg_naive = IFNg_naive, IFNg_both = IFNg_both,
  Salm_naive = Salm_naive, Salm_both = Salm_both
)

deedee_heatmap(dd_list,
  pthresh = 0.05, show_first = 25,
  show_gene_names = FALSE, dist = "euclidean",
  clust = "average", show_na = FALSE
)

lea-rothoerl/DeeDee documentation built on Dec. 21, 2021, 9:47 a.m.