OperaMate (version 1.4.0)

cellViz: Data visualization

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

Value

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

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.

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)