IdMappingAnalysis (version 1.16.0)

plot.CorrData: Scatterplot of experiment data

Description

Scatterplot of experiment data.

Usage

"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 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

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"));