plot.CorrData: Scatterplot of experiment data

In IdMappingAnalysis: ID Mapping Analysis

Description

Scatterplot of experiment data.

Usage

## S3 method for class 'CorrData'
plot(x, input, outcomePairs=NULL, xlab="protein count", ylab="mRNA expression (log10)", method="spearman", proteinNames=NULL, cols=brewer.pal(9, "Set1"), cex=1, cex.main=1.2, cex.lab=1, cex.axis=1, font=1, font.main=3, par.zoom=1, ...)

Arguments

input	character vector of primary IDs, or either vector or list of match pairs.
outcomePairs	The pairs <sample ID, outcome> or NULL (default). In the first case the scatterplot points are plotted with symbol corresponding to the first letter of the outcome keyword. In the second, if there are more than one pair is plotted the point set for each pair is marked as 1, 2, etc. and if there is only one pair is present the unfilled circles are used
xlab	The X axis label. Default is 'protein count'.
ylab	The Y axis label. Default is 'mRNA expression'.
method	the method used to compute the correlation coefficient between X and Y data. Default is "spearman".
proteinNames	extra comments in the plot main title. Default is NULL (no extra comments).
cols	the (recycled) vector of colors to plot each data series with for the particular match pair. Default is RColorBrewer::brewer.pal(9,"Set1").
cex	Plot font size. Default is 1.
cex.main	Main title font size. Default is 1.2.
cex.lab	X and Y titles font size. Default is 1.
cex.axis	X and Y axis labels font size. Default is 1.
font	data points and axis labels font. Default is 2.
font.main	main title font type. Default is 3.
par.zoom	graphics parameters zoom factor. Scales the graphical parameters like cex, lwd, mai etc. Default is 1.
...	Additional graphical parameters

Author(s)

Alex Lisovich, Roger Day

See Also

For more information see CorrData.

Examples

 #scatterplot with outcome for Uniprot="P07355" (annexin 2), probe set ID="213503_x_at"
 examples$corrData$plot(input=list(c("P07355", "213503_x_at")),
	xlab="spectral count",
	outcomePairs=examples$outcomeMap, proteinNames="ANXA2",
	cols=c("green", "red", "darkblue"));
 

IdMappingAnalysis documentation built on Oct. 31, 2019, 3:30 a.m.