Inria SISTM Team

Fingerprint

R Documentation

Function for Finger print plot on Gene set analysis

Description

The aim of this function is to create a visual representation of gene set enrichment results from differential gene expression analysis.

Usage

Fingerprint(
  res_dgsaseq,
  datalog2FC,
  genesets = "Chaussabel",
  category = "immune",
  time = NULL,
  alpha = 0.05,
  title = NULL,
  max_size = 8,
  size_y_lab = 9,
  order_by_pvals = FALSE,
  interactive.plot = FALSE
)

Arguments

`res_dgsaseq`	an object of `dgsa_seq` function in `dearseq` package.
`datalog2FC`	a data.frame with genes in rownames and if (time == NULL) 1 column with Fold Change else several columns are allowed but colnames must contain time's string characters.
`genesets`	a string character "BTM" or "Chaussabel" to use genesets included or an other gmt object. Default is `Chaussabel`.
`category`	a string character or vector. Only needed if `(genesets == "BTM")` : "immune", "signaling", "TF targets", "biological process", "molecular function", "location", "all".
`time`	a string character to filter on time. This time must be present on `datalog2FC`'s colnames. Default is `NULL`.
`alpha`	a numeric corresponding to type 1 error threshold. Default value is `0.05`.
`title`	a string character for plot's title. Default is `NULL`.
`max_size`	a numeric corresponding to the maximum size of point. Default is `8`.
`size_y_lab`	labsize for non-interactive plot, can be useful to set to 0 to combine several plots
`order_by_pvals`	a logical indicating to order genesets per pvalue left to right. Default is `FALSE`.
`interactive.plot`	a logical indicating whether the plot will be interactive, recommended if order_by_pvals is `TRUE`. Default is `FALSE`.