PlotCorrelation: Plot the Correlation Between Phylostrata and Divergence...
In YTLogos/myTAI: Evolutionary Transcriptomics

Description Usage Arguments Value Author(s) References See Also Examples

This function plots the correlation coefficient between phylostratum values and divergence-stratum values of a given PhyloExpressionSet and DivergenceExpressionSet.

This function can be used to test whether a given PS distribution and DS distribution are linear correlated so that the independence of PS and DS can be assumed for subsequent analyses (Quint et al., 2012).

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PlotCorrelation(PhyloExpressionSet, DivergenceExpressionSet,
  method = "pearson", linearModel = FALSE, xlab = "Phylostratum",
  ylab = "Divergencestratum")

`PhyloExpressionSet`	a standard PhyloExpressionSet object.
`DivergenceExpressionSet`	a standard DivergenceExpressionSet object.
`method`	a character string specifying the correlation method to cbe used, e.g. "pearson", "kendall", "spearman".
`linearModel`	a boolean value specifying whether a linear model should be fitted to the data and furthermore, should be visualized in the corresponding plot.
`xlab`	label of x-axis.
`ylab`	label of y-axis.

a jitter-correlation-plot of PS and DS correlation.

Hajk-Georg Drost

Quint M et al. (2012). A transcriptomic hourglass in plant embryogenesis. Nature (490): 98-101. Drost HG et al. (2015) Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis. Mol Biol Evol. 32 (5): 1221-1231 doi:10.1093/molbev/msv012.

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# read standard phylotranscriptomics data
data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)
 
# plot the PS and DS correlation
PlotCorrelation(PhyloExpressionSetExample, 
                DivergenceExpressionSetExample, 
                method      = "pearson", 
                linearModel = TRUE)