volcanoServer: Shiny module for displaying volcano plots

In bihealth/bioshmods: What the Package Does (One Line, Title Case)

Shiny module for displaying volcano plots

Description

Shiny module for displaying volcano plots

Usage

volcanoUI(id, datasets = NULL, lfc_thr = 1, pval_thr = 0.05)

volcanoServer(
  id,
  cntr,
  lfc_col = "log2FoldChange",
  pval_col = "padj",
  primary_id = "PrimaryID",
  annot = NULL,
  gene_id = NULL,
  annot_show = c("SYMBOL", "ENTREZID")
)

Arguments

id	module identifier (same as the one passed to volcanoUI)
datasets	character vector specifying datasets
lfc_thr	default lfc threshold
pval_thr	default p-value threshold
cntr	either a named list of data frames, each being the results of differential expression analysis for one contrast, or a list of data sets, each data set being a named list of data frames.
lfc_col, pval_col	names of the columns in the contrast data frames which hold the log2 fold changes and p-values, respectively
primary_id	name of the primary ID column in contrasts and annotation data frame
annot	data frame with gene annotations (containing at least the column specified with the primary_id parameter) or (if there are multiple data sets) a named list of such data frames. Names of this list must match the names of the cntr list.
gene_id	must be a reactiveValues object. If not NULL, then clicking on a gene identifier will modify this object (possibly triggering an event in another module).
annot_show	which columns from the annotation data frame should be shown when mouse hovers over a gene

bihealth/bioshmods documentation built on July 1, 2023, 4:32 a.m.