PlotRE | R Documentation |
This function computes for each age category the corresponding relative expression profile.
For each age category the corresponding relative expression profile is being computed as follows:
f_js = ( e_js - e_j min ) / ( e_j max - e_j min )
where e_j min
and e_j max
denote the minimum/maximum mean
expression level
of phylostratum j over developmental stages s. This linear transformation corresponds to
a shift by e_j min
and a subsequent shrinkage by e_j max - e_j min
.
As a result, the relative expression level f_js
of developmental stage s
with minimum e_js
is 0, the relative expression level f_js
of the developmental
stage s with maximum e_js
is 1, and the relative expression levels f_js
of
all other stages s range between 0 and 1, accordingly.
PlotRE(
ExpressionSet,
Groups = NULL,
modules = NULL,
legendName = "age",
xlab = "Ontogeny",
ylab = "Relative Expression Level",
main = "",
y.ticks = 10,
adjust.range = TRUE,
alpha = 0.008,
...
)
ExpressionSet |
a standard PhyloExpressionSet or DivergenceExpressionSet object. |
Groups |
a list containing the age categories for which mean expression levels shall be drawn.
For ex. evolutionary users can compare old phylostrata: PS1-3 (Class 1) and evolutionary young phylostrata: PS4-12 (Class 2).
In this example, the list could be assigned as, |
modules |
a list storing three elements for specifying the modules: early, mid, and late.
Each element expects a numeric vector specifying the developmental stages
or experiments that correspond to each module. For example,
|
legendName |
a character string specifying the legend title. |
xlab |
label of x-axis. |
ylab |
label of y-axis. |
main |
main text. |
y.ticks |
number of ticks that shall be drawn on the y-axis. |
adjust.range |
logical indicating whether or not the y-axis scale shall be adjusted to the same range in case two groups are specified. Default is |
alpha |
transparency of the shaded area (between [0,1]). Default is |
... |
place holder for old version of PlotRE that was based on base graphics instead of ggplot2. |
Studying the relative expression profiles of each phylostratum or divergence-stratum enables the detection of common gene expression patterns shared by several phylostrata or divergence-strata.
Finding similar relative expression profiles among phylostrata or divergence-strata suggests that phylostrata or divergence-strata sharing a similar relative expression profile are regulated by similar gene regulatory elements. Hence, these common phylostrata or divergence-strata might govern similar processes in the given developmental time course.
a plot showing the relative expression profiles of phylostrata or divergence-strata belonging to the same group.
Hajk-Georg Drost
Domazet-Loso T and Tautz D. 2010. "A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns". Nature (468): 815-818.
Quint M et al. 2012. "A transcriptomic hourglass in plant embryogenesis". Nature (490): 98-101.
PlotBarRE
, RE
, REMatrix
# read standard phylotranscriptomics data
data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)
# example PhyloExpressionSet
PlotRE(PhyloExpressionSetExample,
Groups = list(c(1:3), c(4:12)),
legendName = "PS")
# or you can choose any combination of groups
PlotRE(PhyloExpressionSetExample,
Groups = list(c(1,7,9), c(2:6,8,10:12)),
legendName = "PS")
# example DivergenceExpressionSet
PlotRE(DivergenceExpressionSetExample,
Groups = list(c(1:5), c(6:10)),
legendName = "DS")
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