happy_hour: Happy hour!

In federicomarini/GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Happy hour!

Description

Start the happy hour, creating a report containing a document full of goodies derived from the provided objects.

Usage

happy_hour(
  dds,
  res_de,
  res_enrich,
  annotation_obj,
  gtl = NULL,
  project_id,
  mygenesets,
  mygenes,
  mygroup = NULL,
  usage_mode = "batch_mode",
  input_rmd = NULL,
  output_file = "my_first_GeneTonic_happyhour.html",
  output_dir = tempdir(),
  output_format = NULL,
  force_overwrite = FALSE,
  knitr_show_progress = FALSE,
  ignore_pandoc = FALSE,
  open_after_creating = TRUE,
  ...
)

Arguments

dds	A DESeqDataSet object, normally obtained after running your data through the DESeq2 framework.
res_de	A DESeqResults object. As for the dds parameter, this is also commonly used in the DESeq2 framework.
res_enrich	A data.frame object, storing the result of the functional enrichment analysis. See GeneTonic() for the formatting requirements.
annotation_obj	A data.frame object with the feature annotation information, with at least two columns, gene_id and gene_name. See GeneTonic() for the formatting requirements.
gtl	A GeneTonic-list object, containing in its slots the arguments specified above: dds, res_de, res_enrich, and annotation_obj - the names of the list must be specified following the content they are expecting
project_id	A character string, which can be considered as an identifier for the set/session, and will be e.g. used in the title of the report created via happy_hour()
mygenesets	A vector of character strings, containing the genesets to focus on in the report - for each geneset, e.g. a signature heatmap can be created.
mygenes	A vector of character strings, containing the genes to focus on in the report - for each gene, the plot of the expression values is included.
mygroup	A character string, or a vector thereof. Contains the experimental variables to be used to split into groups the expression data, and color accordingly.
usage_mode	A character string, which controls the behavior of the Rmd document, based on whether the rendering is triggered while using the app ("shiny_mode"), or offline, in batch mode. Defaults to "batch_mode".
input_rmd	Character string with the path to the RMarkdown (.Rmd) file that will be used as the template for generating the report. Defaults to NULL, which will then use the one provided with the GeneTonic package.
output_file	Character string, specifying the file name of the output report. The file name extension must be either .html or .pdf, and consistent with the value of output_format.
output_dir	Character, defining the path to the output directory where the report will be generated. Defaults to the temp directory (tempdir()).
output_format	The format of the output report. Either html_document or pdf_document. The file name extension of output_file must be consistent with this choice. Can also be left empty and determined accordingly.
force_overwrite	Logical, whether to force overwrite an existing report with the same name in the output directory. Defaults to FALSE.
knitr_show_progress	Logical, whether to display the progress of knitr while generating the report. Defaults to FALSE.
ignore_pandoc	Logical, controlling how the report generation function will behave if pandoc or pandoc-citeproc are missing.
open_after_creating	Logical, whether to open the report in the default browser after being generated. Defaults to TRUE.
...	Other arguments that will be passed to rmarkdown::render().

Details

When happy_hour is called, a RMarkdown template file will be copied into the output directory, and rmarkdown::render() will be called to generate the final report.

As a default template, happy_hour uses the one delivered together with the GeneTonic package, which provides a comprehensive overview of what the user can extract. Experienced users can take that as a starting point to further edit and customize.

If there is already a .Rmd file with the same name in the output directory, the function will raise an error and stop, to avoid overwriting the existing file. The reason for this behaviour is that the copied template in the output directory will be deleted once the report is generated.

Credits to the original implementation proposed by Charlotte Soneson, upon which this function is heavily inspired.

Value

Generates a fully fledged report in the output_dir directory, called output_file and returns (invisibly) the name of the generated report.

See Also

GeneTonic(), shake_topGOtableResult(), shake_enrichResult()

Examples

library("macrophage")
library("DESeq2")
library("org.Hs.eg.db")
library("AnnotationDbi")

# dds object
data("gse", package = "macrophage")
dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)
rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
dds_macrophage <- estimateSizeFactors(dds_macrophage)

# annotation object
anno_df <- data.frame(
  gene_id = rownames(dds_macrophage),
  gene_name = mapIds(org.Hs.eg.db,
    keys = rownames(dds_macrophage),
    column = "SYMBOL",
    keytype = "ENSEMBL"
  ),
  stringsAsFactors = FALSE,
  row.names = rownames(dds_macrophage)
)

# res object
data(res_de_macrophage, package = "GeneTonic")
res_de <- res_macrophage_IFNg_vs_naive

# res_enrich object
data(res_enrich_macrophage, package = "GeneTonic")
res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)
res_enrich <- get_aggrscores(res_enrich, res_de, anno_df)
## Not run: 
happy_hour(
  dds = dds_macrophage,
  res_de = res_de,
  res_enrich = res_enrich,
  annotation_obj = anno_df,
  project_id = "examplerun",
  mygroup = "condition",
  # mygroup = "line",   # alternatively
  mygenesets = res_enrich$gs_id[c(1:5, 11, 31)],
  mygenes = c(
    "ENSG00000125347",
    "ENSG00000172399",
    "ENSG00000137496"
  )
)

## End(Not run)

federicomarini/GeneTonic documentation built on Oct. 10, 2024, 8:49 p.m.