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

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

## -----------------------------------------------------------------------------
#  CCNB1xml <- hpaXmlGet("ENSG00000134057")
#  
#  CCNB1_ab <- hpaXmlAntibody(CCNB1xml)
#  CCNB1_ab
#  #> # A tibble: 4 x 4
#  #>   id        releaseDate releaseVersion RRID
#  #>   <chr>     <chr>       <chr>          <chr>
#  #> 1 CAB000115 2006-03-13  1.2            <NA>
#  #> 2 CAB003804 2006-10-30  2              AB_562272
#  #> 3 HPA030741 2013-12-05  12             AB_2673586
#  #> 4 HPA061448 2016-12-04  16             AB_2684522
#  
#  CCNB1_expr <- hpaXmlTissueExpr(CCNB1xml)
#  str(CCNB1_expr[[1]])
#  #> Classes 'tbl_df', 'tbl' and 'data.frame':    331 obs. of  18 variables:
#  #>  $ patientId         : chr  "1653" "1721" "1725" "598" ...
#  #>  $ age               : chr  "53" "60" "57" "7" ...
#  #>  $ sex               : chr  "Male" "Female" "Male" "Male" ...
#  #>  $ staining          : chr  NA NA NA NA ...
#  #>  $ intensity         : chr  NA NA NA NA ...
#  #>  $ quantity          : chr  NA NA NA NA ...
#  #>  $ location          : chr  NA NA NA NA ...
#  #>  $ imageUrl          : chr  "http://v18.proteinatlas.org/images/115/2043_B_4_5.jpg" "http://v18.proteinatlas.org/images/115/2043_B_6_5.jpg" "http://v18.proteinatlas.org/images/115/2043_B_5_5.jpg" "http://v18.proteinatlas.org/images/115/2043_A_2_2.jpg" ...
#  #>  $ snomedCode1       : chr  "M-00100" "M-00100" "M-00100" "M-00100" ...
#  #>  $ snomedCode2       : chr  "T-93000" "T-93000" "T-93000" "T-66000" ...
#  #>  $ snomedCode3       : chr  NA NA NA NA ...
#  #>  $ snomedCode4       : chr  NA NA NA NA ...
#  #>  $ snomedCode5       : chr  NA NA NA NA ...
#  #>  $ tissueDescription1: chr  "Normal tissue, NOS" "Normal tissue, NOS" "Normal tissue, NOS" "Normal tissue, NOS" ...
#  #>  $ tissueDescription2: chr  "Adrenal gland" "Adrenal gland" "Adrenal gland" "Appendix" ...
#  #>  $ tissueDescription3: chr  NA NA NA NA ...
#  #>  $ tissueDescription4: chr  NA NA NA NA ...
#  #>  $ tissueDescription5: chr  NA NA NA NA ...

## ----eval=FALSE---------------------------------------------------------------
#  dir.create("img")
#  for (i in 1:nrow(CCNB1_expr[[1]])) {
#      download.file(CCNB1_expr[[1]]$imageUrl[i],
#                    destfile = paste0("img/", CCNB1_ab$id[1], "_",
#                                      CCNB1_expr[[1]]$patientId[i], "_",
#                                      CCNB1_expr[[1]]$tissueDescription2[i],
#                                      ## the extra i below ensures unique file name
#                                      i, ".jpg"),
#                    mode = "wb")
#  }

