doViolin: Generates the Violin plot

In dianalow/nMyo: nMyo

Description

It creates the Violin plot of a marker for the cell types of interest

Usage

doViolin(
  Data,
  grouping.by = "CellType",
  grouping2.by = "Condition",
  size = 5,
  show.plot = TRUE,
  save.plot = FALSE,
  save.table = FALSE,
  interactive = TRUE
)

Arguments

Data	list. The outcome of MarkerQuery().
grouping.by	character. A grouping variable to be depicted in the plot. It groups (color code) the samples with common values for this variable. It can take any of the factor variables depicted at the column names of Data$Design. Default is CellType.
grouping2.by	character. A grouping variable to split each violin plot. Default is Condition.
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<-doViolin(Data=data,
         show.plot=TRUE,
         save.plot=FALSE)

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