Visualisation function of the SpeCond analysis results

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Description

getFullHtmlSpeCondResult generates a full result html page.

Usage

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getFullHtmlSpeCondResult(SpeCondResult=NULL, L.specific.result = NULL, 
param.detection = NULL, page.name = "SpeCond_result",
page.title = "Condition-specific analysis results", prefix.file = NULL, 
outdir="General_Result", sort.condition = "all", 
gene.page.info=NULL, heatmap.profile = TRUE, heatmap.expression = FALSE, 
heatmap.unique.profile = FALSE, expressionMatrix = NULL)

Arguments

SpeCondResult

the sp_list class object result of the SpeCond functions

L.specific.result

List of results present in the sp_list class specificResult object, see SpeCond or getSpecificResult functions

param.detection

The parameter matrix used by the SpeCond detection procedure

page.name

The name of the result html page. The default is "SpeCond\_result"

page.title

The title of the result html page. The default is "Condition-specific analysis results"

prefix.file

a prefix added to the generated file(s) and the outdir directory name to linked them to the full result html page, by default is NULL, the prefix.file attribute of the SpeCondResult is used. It is useful to change the prefix when you create a new result page. As you may want to get results with different parameter sets and plots so using a different SpeCondResult or L.specific.result objects

outdir

the name of the directory in which the generated files will be created. The default is "General_result"

sort.condition

If the condition must sorted in the barplot presented the number of specific genes by condition. Can table the values: positive", "negative", "all": the conditions are sorted respectively by the number of specific genes detected as up-regulated, down-regulated or both

gene.page.info

the result of the getGeneHtmlPage function. Enables the creation of links between this full result page and the single result pages created by the previous function. The default is "NULL"; no links are created

heatmap.profile

TRUE/FALSE, to print or not a heatmap showing the specific profile of the genes. The default is FALSE

heatmap.expression

TRUE/FALSE, to print or not a heatmap showing the expression of the genes. The default is FALSE

heatmap.unique.profile

TRUE/FALSE, to print or not a heatmap showing the unique specific profile. The default is FALSE

expressionMatrix

Must not be NULL if heatmap.expression=TRUE, must be the same as the input expression matrix. The default is NULL

Details

Either SpeCondResult or L.specific.result can be specified to use this function. If you use L.specific.result you ahve tp define prefix.file.

Author(s)

Florence Cavalli, florence@ebi.ac.uk

See Also

getGeneHtmlPage

Examples

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library(SpeCond)
data(expressionSpeCondExample)
##Perform the condition specific detection analysis with SpeCond()
generalResult=SpeCond(expressionSpeCondExample, param.detection=NULL, 
		        multitest.correction.method="BY", prefix.file="E", print.hist.pv=TRUE, 
                        fit1=NULL, fit2=NULL, specificOutlierStep1=NULL)

specificResult=generalResult$specificResult

##Produce the general html page results
getFullHtmlSpeCondResult(SpeCondResult=generalResult, param.detection=	
  specificResult$param.detection, page.name="Example_SpeCond_results",
  page.title="Tissue specific results", sort.condition="all", heatmap.profile=TRUE,
  heatmap.expression=FALSE, heatmap.unique.profile=FALSE, 
  expressionMatrix=expressionSpeCondExample)

##Produce the Gene html page results for the first 20 genes using the specificResult object to be able to link 
## these pages to the table result in the general html page
specificResult=generalResult$specificResult
genePageInfo=getGeneHtmlPage(expressionSpeCondExample, specificResult, name.index.html=
  "index_example_SpeCond_Results.html",outdir="Single_result_pages_example", 
   gene.html.ids=c(1:20))

##Produce the general html page results
getFullHtmlSpeCondResult(L.specific.result=specificResult$L.specific.result,
  param.detection=specificResult$param.detection, page.name="Example_SpeCond_results2",
  page.title="Tissue specific results", prefix.file="S2", sort.condition="all",
  heatmap.profile=TRUE, heatmap.expression=FALSE, heatmap.unique.profile
  =FALSE, expressionMatrix=Mexp, gene.page.info=genePageInfo)