cellViz: Data visualization

In OperaMate: An R package of Data Importing, Processing and Analysis for Opera High Content Screening System

Description

Visualize data by heatmap or boxplot.

Usage

cellViz(object, data.type = c("raw", "norm"), plot = c("heatmap",
  "boxplot"), outpath = getOption("opm.outpath"), multiplot = FALSE,
  plateID = NULL, tag = NULL, ctr.excluded = TRUE, ...)

Arguments

object	a cellData object
data.type	c("raw", "norm), visualizing both types by default
plot	c("heatmap","boxplot")
outpath	directory of output figures, default: getOption("opm.outpath")
multiplot	logical, the output images are placed in one figure or not
plateID	numeric or character
tag	character, unique tag for one figure
ctr.excluded	logical, if controls are included in the visualization
...	other arguments for graphical devices and pheatmap

Details

By visualizing the raw data, users can observe the batch effects as a large region of distinguishing color in heatmap or biased distribution by boxplots. Users can also visualize thr normalized data for comparison.

Value

Invisibly a list of the values returned by pheatmap and ggplot2 function for boxplot

Examples

data(demoCell)
op <- options("device")
options("device" = "png")
cellViz(oneCell, data.type = c("raw", "norm"), plateID = 1:6, outpath = tempdir())
cellViz(oneCell, data.type = c("raw", "norm"), plateID = 1, outpath = tempdir())
options(op)

OperaMate documentation built on Nov. 17, 2017, 1:55 p.m.