plot_ES: Plots Enrichment Score from the output of GSEA.run.

In LauraPS1/TFEA.ChIP: Analyze Transcription Factor Enrichment

Plots Enrichment Score from the output of GSEA.run.

Description

Function to plot the Enrichment Score of every member of the ChIPseq binding database.

Usage

plot_ES(
  GSEA_result,
  LFC,
  plot_title = NULL,
  specialTF = NULL,
  TF_colors = NULL,
  Accession = NULL,
  TF = NULL
)

Arguments

GSEA_result	Returned by GSEA_run
LFC	Vector with log2(Fold Change) of every gene that has an Entrez ID. Arranged from higher to lower.
plot_title	(Optional) Title for the plot
specialTF	(Optional) Named vector of TF symbols -as written in the enrichment table- to be highlighted in the plot. The name of each element specifies its color group, i.e.: naming elements HIF1A and HIF1B as 'HIF' to represent them with the same color.
TF_colors	(Optional) Colors to highlight TFs chosen in specialTF.
Accession	(Optional) restricts plot to the indicated list dataset IDs.
TF	(Optional) restricts plot to the indicated list transcription factor names.

Value

Plotly object with a scatter plot -Enrichment scores- and a heatmap -log2(fold change) bar-.

Examples

data('GSEA.result','log2.FC',package = 'TFEA.ChIP')
TF.hightlight <- c('E2F1' = 'E2F1')
col <- c('red')
plot_ES( GSEA.result, log2.FC, "Example", TF.hightlight, col )

LauraPS1/TFEA.ChIP documentation built on April 21, 2023, 7:29 a.m.