inst/doc/phantasus-tutorial.R

In phantasus: Visual and interactive gene expression analysis

## ----eval=FALSE---------------------------------------------------------------
#  library(phantasus)
#  servePhantasus()

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knitr::include_graphics("images/start_screen.jpg")

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knitr::include_graphics("images/dataset_loaded.jpg")

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knitr::include_graphics("images/huge_value.jpg")

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knitr::include_graphics("images/adjust_tool.jpg")

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knitr::include_graphics("images/duplicates.jpg")

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knitr::include_graphics("images/collapse_tool.jpg")

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knitr::include_graphics("images/calculated_annotation_tool.jpg")

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knitr::include_graphics("images/calculated_annotation_loaded.jpg")

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knitr::include_graphics("images/filter_tool.jpg")

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knitr::include_graphics("images/filter_tool_result.jpg")

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knitr::include_graphics("images/pcaplot_tool_clean.png")

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knitr::include_graphics("images/pcaplot_tool_finished.png")

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knitr::include_graphics("images/kmeans_tool.jpg")

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knitr::include_graphics("images/kmeans_result.jpg")

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knitr::include_graphics("images/hierarchical_tool.jpg")

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knitr::include_graphics("images/good_samples.jpg")

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knitr::include_graphics("images/limma_tool.jpg")

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knitr::include_graphics("images/limma_results.png")

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knitr::include_graphics("images/fgsea_tool.png")

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knitr::include_graphics("images/fgsea_result.png")

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knitr::include_graphics("images/annotation_tool.png")

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knitr::include_graphics("images/annotation_result.png")

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knitr::include_graphics("images/enrichr.png")

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knitr::include_graphics("images/enrichr_result.png")

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knitr::include_graphics("images/shiny_gam.jpg")

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knitr::include_graphics("images/shiny_gam_result.jpg")

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knitr::include_graphics("images/fgsea_genes.png")

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knitr::include_graphics("images/fgsea_search.png")

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knitr::include_graphics("images/GSEA_plot.png")

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knitr::include_graphics("images/link.png")

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knitr::include_graphics("images/open_file_tool.jpg")

## ---- message=FALSE, cache=TRUE, eval=FALSE-----------------------------------
#  library(GEOquery)
#  library(limma)
#  gse14308 <- getGEO("GSE14308", AnnotGPL = TRUE)[[1]]
#  gse14308$condition <- sub("-.*$", "", gse14308$title)
#  pData(gse14308) <- pData(gse14308)[, c("title", "geo_accession", "condition")]
#  gse14308 <- gse14308[, order(gse14308$condition)]
#  
#  fData(gse14308) <- fData(gse14308)[, c("Gene ID", "Gene symbol")]
#  exprs(gse14308) <- normalizeBetweenArrays(log2(exprs(gse14308)+1), method="quantile")
#  
#  ess <- list(GSE14308_norm=gse14308)
#  
#  preloadedDir <- tempdir()
#  
#  save(ess, file=file.path(preloadedDir, "GSE14308_norm.rda"))

## ---- eval=F------------------------------------------------------------------
#  servePhantasus(preloadedDir=preloadedDir)

## ---- out.width="650px", echo = FALSE-----------------------------------------
knitr::include_graphics("images/gse14308_norm.png")

## ---- eval=F------------------------------------------------------------------
#  updateARCHS4(cacheDir=cacheDir)

## ---- eval=TRUE---------------------------------------------------------------
data("fgseaExample", package="phantasus")
head(fgseaExample)