## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
  collapse=TRUE,
  comment="#>",
  warning=FALSE,
  error=FALSE,
  crop = NULL
)

## ----library, message=FALSE, warning=FALSE, error=FALSE-----------------------
# library(BiocStyle)
library(HPAanalyze)
library(dplyr)

## ----hpaVis_eg----------------------------------------------------------------
hpaVis(targetGene = c("GCH1", "PTS", "SPR", "DHFR"),
       targetTissue = c("Cerebellum", "Cerebral cortex", "Hippocampus"),
       targetCancer = c("glioma"))

## ----hpaVis_eg2, eval = FALSE-------------------------------------------------
# hpaVis()
# 
# # No data provided. Use version ...
# # targetGene variable not specified, default to TP53, RB1, MYC, KRAS and EGFR.
# # targetTissue variable not specified, default to breast.
# # targetCellType variable not specified, visualize all.
# # * WARNING: targetCellType variable not specified, visualize all.
# # >> Use hpaListParam() to list possible values for target variables.
# # targetCancer variable not specified, default to breast cancer
# # Use hpaListParam() to list possible values for target variables.
# 

## ----hpaVis_eg3---------------------------------------------------------------
hpaVis(visType = "Patho",
       targetGene = c("GCH1", "PTS", "SPR", "DHFR"),
       targetCancer = c("glioma", "breast cancer"))

## ----hpaVisPatho_eg-----------------------------------------------------------
hpaVisPatho(targetGene = c("GCH1", "PTS", "SPR", "DHFR"))

## ----doc_ex1, eval = FALSE----------------------------------------------------
# ?hpaVis # the easy umbrella to visualize protein expression levels
# ?hpaVisTissue # in normal tissue
# ?hpaVisSubcell # in subcellular compartments
# ?hpaVisPatho # in cancers

## ----listParam_ex, eval = FALSE-----------------------------------------------
# hpaListParam()

## ----listParam_ex2, echo= FALSE-----------------------------------------------
hpaListParam() %>% glimpse()

## ----eval=FALSE---------------------------------------------------------------
# EGFR <- hpaXml(inputXml='ENSG00000146648')
# names(EGFR)
# 
# #> [1] "ProtClass"     "TissueExprSum" "Antibody"      "TissueExpr"

## ----doc_ex2, eval = FALSE----------------------------------------------------
# ?hpaXmlGet # import the xml file as "xml_document"
# ?hpaXmlProtClass
# ?hpaXmlTissueExprSum
# ?hpaXmlAntibody
# ?hpaXmlTissueExpr