getFullHtmlSpeCondResult {SpeCond} | R Documentation

## Visualisation function of the SpeCond analysis results

### Description

`getFullHtmlSpeCondResult` generates a full result html page.

### Usage

    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

    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)

[Package SpeCond version 1.34.0 Index]