deedee_summary: DeeDee Summary

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

Description

DeeDee Summary

Usage

deedee_summary(
  deedee_list,
  output_path = "DeeDee_Summary.html",
  overwrite = FALSE,
  pthresh = 0.05,
  scatter_select1 = 1,
  scatter_select2 = 2,
  scatter_color_by = "pval1",
  heatmap_show_first = 25,
  heatmap_show_gene_names = FALSE,
  heatmap_dist = "euclidean",
  heatmap_clust = "average",
  heatmap_show_na = FALSE,
  venn_mode = "both",
  upset_mode = "both_colored",
  upset_min_setsize = 10,
  qqmult_ref = 1,
  cat_ref = 1,
  cat_maxrank = 1000,
  cat_mode = "up",
  silent = FALSE,
  open_file = TRUE
)

Arguments

deedee_list	named list of results from deedee_prepare()
output_path	the path to save the resulting report in. must end with a filename.html (default = "DeeDee_Summary.html" in the working directory)
overwrite	logical value specifying if the output is supposed to overwrite a potential existing file at the location of output_path (default = FALSE)
pthresh	threshold for p-values to be in-/excluded (default = 0.05)
scatter_select1	index of first data-list element to be used (default = 1)
scatter_select2	index of second data-list element to be used (default = 2)
scatter_color_by	indicates which set of values the output should be colored by (possible values = pval1 (default), pval2)
heatmap_show_first	indicating the number of genes depicted (default = 25)
heatmap_show_gene_names	boolean, show row names next to heatmap (default = FALSE)
heatmap_dist	select the distance measure (euclidean, manhattan, pearson, spearman)
heatmap_clust	select the clustering method (single, complete, average, centroid)
heatmap_show_na	boolean, include genes with NA values in heatmap (default = FALSE)
venn_mode	show all overlapping DE genes (both, default), only conjointly up-regulated (up) or only conjointly down-regulated (down) genes
upset_mode	show all overlapping DE genes (both), all overlapping genes colored by DE direction (both_colored, default), only conjointly up-regulated (up) or only conjointly down-regulated (down) genes
upset_min_setsize	the minimum size of intersections to be displayed in the UpSet plot (default = 10)
qqmult_ref	index of the contrast in data to be used as reference contrast (default = 1)
cat_ref	index of the contrast in data to be used as reference contrast (default = 1)
cat_maxrank	highest rank that should be displayed (default = 1000)
cat_mode	sort by highest logFC (up, default), lowest logFC (down) or greatest deviation from zero (both)
silent	logical, specifying if success message shall be suppressed (default = FALSE)
open_file	logical, specifying if the output file is supposed to be opened after successful creation (default = TRUE)

Value

Creates a html document containing the results of running the DeeDee functions on your input data and params. TODO where

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
)
## Not run: 
deedee_summary(dd_list)

## End(Not run)

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