Description Usage Arguments Details Value Author(s) See Also
View source: R/functions_comp2annottests.R
This internal function creates an HTML file containing a
table of dimensions 'variables x components' with
pvalues. When a pvalue is considered as significant
according to the threshold cutoff
, it is written
in bold and filled with a link pointing to the
corresponding plot. These plots are contained in images
located in the path pathplot
. To be identified by
the function, the file syntax of each image file must be
"indexofcomponent_colAnnot.typeImage".
1 2 3 4 5 6  writeHtmlResTestsByAnnot(params, icaSet, res, res2,
nameres = "p", nameres2 = "cor", onlySign = TRUE,
cutoff = params["pvalCutoff"],
cutoffDir = c("<=", ">="), path, pathplot = "plots/",
filename = NULL, typeImage = "png", caption = "",
keepVar)

params 
An object of class

icaSet 
An object of class

res 
A matrix or data.frame of dimension
'components x variables' containing numeric values that
quantify the association of the components with sample
variables (e.g pvalues, FDR, correlation values). This
is the matrix used to select the significant results
according to 
res2 
A matrix or data.frame of dimension 'components x variables' containing numeric values that quantify the association of the components with sample annotations (e.g pvalues, FDR, correlation values). It is only used as an additional result displayed in the output. 
nameres 
Name of the values contained in

nameres2 
Name of the values contained in

onlySign 
If TRUE (default), only the significant results are plotted 
cutoff 
The threshold pvalue for statistical significance 
path 
A directory for the HTML file containing the pvalue results 
pathplot 
A directory for the plots 
filename 
The name of the file where the results will be displayed in format HTML, if NULL no file is created 
typeImage 
The type of image file where each plot is saved 
caption 
The title of the HTML table 
cutoffDir 
The direction to be used with the
cutoff: 
keepVar 
The variable labels to be considered, i.e
a subset of the variables of icaSet available in

If argument onlySign
is TRUE, then only links to
plots that are significant according to the given
threshold are provided.
When res2
is not missing, the values contained in
res2
are pasted to the values contained in res in
the output array. nameres
and nameres2
are
used such as every element in the ouput array contains
two indexed values: nameres
=x, nameres2
=y.
Returns a data.frame of dimensions 'components x variables' containing the pvalues of the nonparametric tests (Wilcoxon or KruskalWallis tests) wich test if the samples groups defined by each variable are differently distributed on the components
Anne Biton
p.adjust
, qualVarAnalysis
,
quantVarAnalysis
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