Usage
anotaPlotSigGenes(anotaSigObj, selIds=NULL, selContr=NULL, minSlope=NULL, maxSlope=NULL, slopeP=NULL, minEff=NULL, maxP=NULL, maxPAdj=NULL, maxRvmP=NULL, maxRvmPAdj=NULL, selDeltaPT=NULL, selDeltaP=NULL, sortBy=NULL, performPlot=TRUE, fileName="ANOTA_selected_significant_genes_plot.pdf", geneNames=NULL)
Arguments
anotaSigObj
The output from the anotaGetSigGenes function.
selIds
The function can consider only a subset of the
identifiers from the input data set (which can be further filtered)
or used for custom plotting of identifiers of interest (leaving all
filters as NULL). For custom selection of identifiers, supply a vector of identifiers
(row names from the original data set) to be
included. Default is NULL i.e. filtering is performed on all
identifiers. Minimum length of selIds is currently 2. However, if
only one identifier is of interest this identifier can be at
position one and two of the supplied vector which will lead to that
the data for the identifier of interested will be plotted twice.
selContr
Which contrast should be evaulated during the
filtering, sorting and plotting? Descriptions of
the contrasts can be found in the output from the anotaGetSigGenes
object in the usedContrasts slot. Indicate the contrast by the column
number.
minSlope
The output can be filtered so that genes whose
identified slopes are too small can be excluded. Default is NULL
i.e. no filtering based on lower boundary of the slope. To exclude
genes with e.g. a slope
maxSlope
The output can be filtered so that genes whose
identified slopes are too large can be excluded. Default is NULL
i.e. no filtering based on upper boundary of the slope. To exclude
genes with e.g. a slope >2 assign 2 to maxSlope.
slopeP
A p-value for the slope being <0 or="">1 is calculated if the estimate
for the slope is <0 or="">1. This p-value can be used to
filter the output based on unrealistic slopes. When set low fewer
genes will be disqualified. Default is NULL i.e. no filtering based
on slope p-value. We recommend setting slopeP between 0.01 and 0.1
depending on data set characteristics.
minEff
The output can be filtered based on minimum effect for
inclusion. The value is applied both to negative and positive effects:
e.g. a value of 1 will evaluate if the effects are >1 OR
maxP
The output can be filtered based on raw p-values from the
anota analysis without RVM (i.e. smaller compared to assigned
value). Default is NULL i.e. no filtering.
maxPAdj
The output can be filtered based on adjusted p-values from the
anota analysis without RVM (i.e. smaller compared to assigned
value). The adjustment method that was used when running
anotaGetSigGenes will be evaluated. Default is NULL i.e. no filtering.
maxRvmP
The output can be filtered based on raw p-values from the
anota analysis with RVM (i.e. smaller compared to assigned
value). Default is NULL i.e. no filtering.
maxRvmPAdj
The output can be filtered based on adjusted p-values from the
anota analysis with RVM (i.e. smaller compared to assigned value). The
adjustment method that was used when running
anotaGetSigGenes will be evaluated. Default is NULL i.e. no filtering.
selDeltaPT
The output can be filtered based on the mean log2(translational
activity data / cytosolic mRNA data) between groups difference. The
groups are defined by the selected contrast. Default is
NULL i.e. no filtering.
selDeltaP
The output can be filtered based on the translational
activity data only so that the minimum absolute between groups delta
translation is used for gene inclusion. The groups are defined by
the selected contrast. Default is NULL i.e. no filtering.
sortBy
The output can be sorted by effect ("Eff"), raw
p-value("p") or raw RVM p-value ("apvRvmP"). Default is NULL i.e. no sorting.
performPlot
The function can generate a graphical output per
gene. Default is TRUE i.e. generate plots.
fileName
The plots are printed to a file whose file name is
given here. Default is "ANOTA_selected_significant_genes_plot.pdf".
geneNames
When anotaPlotSigGenes plots the individual gene plots
they will be named by the original row names supplied to the
anotaGetSigGenes function. geneNames allows the user to add additional
names when plotting to e.g. include gene symbols. Input is a matrix
with one column where the original row names match the row names of the input matrix and
the desired new names are given in column 1. Default is NULL
i.e. no additional names.