doVolcano: Generates the Volcano plot

In dianalow/nMyo: nMyo

Description

It creates the Volcano plot for a particular cell type and condition

Usage

doVolcano(
  Data,
  filters,
  logFC = 1,
  FDR = 0.01,
  show.more = FALSE,
  size = 5,
  show.plot = TRUE,
  save.plot = FALSE,
  save.table = FALSE,
  interactive = TRUE
)

Arguments

Data	list. The outcome of MarkerQuery().
filters	character. A set of conditions that specifies which differential expression results should be plotted. It should ALWAYS be a level of the Comparison variable of the DEstats component.
logFC	numeric. A positive value specifying the symmetric logFC cut-off to be depicted. Default is 1.
FDR	numeric. A value between (0,1] specifying the FDR cutoff to be depicted. Default is 0.01.
show.more	logical. If TRUE, all markers of Data$filteredData$Marker_List are highlighted, otherwise only the marker of Data$selectedData$Marker_List is highlighted. Default is FALSE.
size	numeric. It specifies the plotted dot size. Default is 5.
show.plot	logical. If TRUE, it shows the plot on the screen. Default is TRUE.
save.plot	logical. If TRUE, it saves the plot in an automatically generated folder <data folder>/Output/<InteractivePlots or NonInteractivePlots>. Default is FALSE.
save.table	logical. If TRUE, it saves the plot in an automatically generated folder <data folder>/Output/Tables. Default if FALSE.
interactive	logical. If TRUE, it generates an interactive plot with plotly otherwise a static plot with ggplot. Default is TRUE.

Value

data list. The plots and the tables of interest stored in automatically generated <data folder>/Output/ folders. The tables include a summary table of quantiles of the marker expression, the differential expression analysis results of the markers of interest and the normalised data for the markers of interest.

Examples

data(nMyo_Data)
data<-readData(nMyo_Data,Markers_file=NULL,is.Exact=TRUE,logFC_cutoff=0,FDR_cutoff=1)

data<-MarkerQuery(Data=data,marker="Postn")

data<-doVolcano(Data=data,
         filters="Comparison=='Fibroblast: Sham-MI'",
         logFC=1,
         FDR=0.01,
         show.plot=TRUE,
         save.plot=FALSE)

dianalow/nMyo documentation built on June 2, 2020, 12:03 a.m.