GPrank (version 0.1.4)

bitseq_plotGP: Plotting fitted GP models for the BitSeq example

Description

Function for plotting GP profiles. If the item to be plotted has multiple items which are associated with itself, its items can be plotted on top of each other by setting multi to 1, for better visual comparison. Log Bayes factors are displayed in legends for at most three items which have the largest log Bayes factors.

Usage

bitseq_plotGP(item, GPfits, gpData, multi = 0, ylimits = NULL,
  x_ticks = NULL, x_label = NULL, y_label = NULL, plotName = NULL,
  colScale = getColorVector())

Arguments

item

Name of the item whose GP profile to be plotted.

GPfits

List structure obtained by bitseq_fitGPs which contains the time-independent and time-dependent GP models for specified (?) item.

gpData

List structure obtained by, for example, bitseq_rnaSeqData function.

multi

Indicator value for specifying whether multiple plots (1) or a single plot (0) will be plotted on the same frame. Default value is 0.

ylimits

Numeric vector which contains minimum and maximum limits for the y axis.

x_ticks

X-axis tick labels.

x_label

X-axis label.

y_label

Y-axis label.

plotName

Name of the plot containing png or pdf extension. png is recommended for the plots which will be displayed on the browser, whereas pdf is recommended for the plots which will be used in printed documents. The default plotting settings are specified in bitseq_setPlot function. If you would like to use your own preferred settings, remember to specify them on your own.

colScale

RGB color code of the plot. If not specified, colors are determined by default.

Value

GP plot(s) for the given item.

See Also

getColorVector bitseq_setPlot bitseq_fitGPs bitseq_rnaSeqData

Examples

# NOT RUN {
RNAseqDATA
gpData=RNAseqDATA$reltr
GPfits=bitseq_fitGPs(gpData)
item="ARAP2"
multi=1
ylimits=c(0,1)
x_ticks=c("0","5","10","20","40","80","160","320","640","1280")
x_label="Time (minutes)"
y_label="Expression level (rpkm)"
plotName="ARAP2_reltr.pdf"
bitseq_plotGP(item, GPfits, gpData, multi, ylimits, x_ticks, x_label, y_label, plotName)
# }
# NOT RUN {
# }