View source: R/PlotSignatureTransformed.R
PlotSignatureTransformed | R Documentation |
PlotSignatureTransformed aims to statistically evaluate the
stability of ReductiveHourglassTest
, FlatLineTest
,
ReverseHourglassTest
, EarlyConservationTest
, or
LateConservationTest
(all based on TAI
or TDI
computations) against different
data transformations AND plot the resulting TAI profiles using PlotSignature
.
The corresponding p-value quantifies the probability that a given TAI or TDI pattern (or any phylotranscriptomics pattern)
does not support the chosen test. A p-value < 0.05 indicates that the corresponding phylotranscriptomics pattern does
indeed support the chosen test.
PlotSignatureTransformed(
ExpressionSet,
measure = "TAI",
TestStatistic = "FlatLineTest",
transforms = c("none", "sqrt", "log2", "rank", "squared"),
modules = NULL,
permutations = 1000,
pseudocount = 1,
p.value = TRUE,
shaded.area = FALSE,
xlab = "Ontogeny",
ylab = "Transcriptome Index",
main = "",
lwd = 4,
alpha = 0.1,
y.ticks = 3
)
ExpressionSet |
a standard PhyloExpressionSet or DivergenceExpressionSet object. |
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:
|
transforms |
a character vector of any valid function that transforms gene expression levels. Available options are:
|
modules |
a list storing three elements for the
|
permutations |
a numeric value specifying the number of permutations to be performed for the |
pseudocount |
any valid number to add to the expression matrix prior to log transformations. |
p.value |
a boolean value specifying whether the p-value of the test statistic shall be printed within the plot area. |
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 (between [0,1]). Default is |
y.ticks |
number of ticks on the y-axis. Default is |
Visualisation and assessment for the stability of data transforms on the permutation test of choice.
For details, please consult the main function PlotSignature
,
as well as tf
, ReductiveHourglassTest
,
FlatLineTest
, ReverseHourglassTest
,
LateConservationTest
or EarlyConservationTest
.
In most cases, users can replace PlotSignature
simply with
PlotSignatureTransformed
to obtain the multi-panel plot with different
transformations to visualise the stability of the pattern observed with PlotSignature
.
a ggplot object containing the following information
for each visualised transcriptome indices:
p.value
: the p-value quantifying the statistical significance (depending on the chosen test) of the given phylotranscriptomics pattern.
Jaruwatana Sodai Lotharukpong
Lotharukpong JS et al. (2023) (unpublished)
PlotSignature
,tfStability
,
FlatLineTest
, ReverseHourglassTest
,
EarlyConservationTest
, ReductiveHourglassTest
,
LateConservationTest
## Not run:
data(PhyloExpressionSetExample)
# Flat line test
PlotSignatureTransformed(ExpressionSet = PhyloExpressionSetExample,
TestStatistic = "FlatLineTest",
transforms = c("none", "log2", "sqrt", "rank", "squared"))
# Reductive hourglass test
PlotSignatureTransformed(ExpressionSet = PhyloExpressionSetExample,
TestStatistic = "ReductiveHourglassTest",
transforms = c("none", "log2", "sqrt", "rank", "squared"),
modules = list(early = 1:2, mid = 3:5, late = 6:7))
library(DESeq2)
PlotSignatureTransformed(ExpressionSet = PhyloExpressionSetExample,
TestStatistic = "ReductiveHourglassTest",
transforms = c("none", "log2", "sqrt", "vst", "rank", "squared"),
modules = list(early = 1:2, mid = 3:5, late = 6:7))
## End(Not run)
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