View source: R/PlotSignatureGeneQuantiles.R
PlotSignatureGeneQuantiles | R Documentation |
PlotSignatureGeneQuantiles is used to investigate the robustness of a transcriptomic index signal to removing the most highly expressed genes from the given expression set. The resulting perturbed signal is plotted for different quantile probability thresholds defining the set of top level genes.
PlotSignatureGeneQuantiles(
ExpressionSet,
quantiles = c(1, 0.99, 0.95, 0.9, 0.8),
gene.selection.criterion = "mean",
measure = "TAI",
TestStatistic = "FlatLineTest",
modules = NULL,
permutations = 1000,
p.value = TRUE,
shaded.area = FALSE,
xlab = "Ontogeny",
ylab = "Transcriptome Index",
main = "",
lwd = 4,
alpha = 0.1,
y.ticks = 3
)
ExpressionSet |
a standard PhyloExpressionSet, DivergenceExpressionSet or PolymorphismsExpressionSet object. |
quantiles |
a numeric vector of quantile probabilities (between [0,1]) |
gene.selection.criterion |
a string defining the criterion by which genes should be selected Possible values can be:
|
measure |
type of transcriptome index that shall be computed. E.g.
|
TestStatistic |
a string defining the type of test statistics to be used to quantify the statistical significance the present phylotranscriptomics pattern. Possible values can be:
|
modules |
a list storing three elements for the
|
permutations |
a numeric value specifying the number of permutations to be performed for the |
p.value |
a boolean value specifying whether the p-value of the test statistic shall be printed within the legend, for each expression set. |
shaded.area |
a boolean value specifying whether a shaded area shall be drawn for the developmental stages defined to be the presumptive phylotypic period. |
xlab |
label of x-axis. |
ylab |
label of y-axis. |
main |
figure title. |
lwd |
line width. |
alpha |
transparency of the shaded area and error ribbon (between [0,1]). Default is |
y.ticks |
number of ticks on the y-axis. Default is |
a ggplot object visualising the transcriptome index of the expression set, together with its standard deviation per stage, obtained by permuting the gene ages. For each quantile probability threshold, the resulting perturbed signal is shown as a separate profile. The profiles are shown on the same axes, so that they can be readily compared. Optionally, the p-value of each profile, with respect to the choice of statistic, is shown.
Stefan Manolache
data(PhyloExpressionSetExample)
# Flat line test, select top expressed genes
PlotSignatureGeneQuantiles(ExpressionSet = PhyloExpressionSetExample,
quantiles=c(1.0, 0.99, 0.95, 0.90, 0.80),
main="Excluding top level genes by total
expression using different thresholds",
gene.selection.criterion="mean")
# Flat line test, select top genes by variance of expression
PlotSignatureGeneQuantiles(ExpressionSet = PhyloExpressionSetExample,
main="Excluding top level genes by variance of
expression using different thresholds",
quantiles=c(1.0, 0.99, 0.95, 0.90, 0.80),
gene.selection.criterion="variance")
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