---
title: "6. Tutorial: Download histology images from the Human Protein Atlas"
author:
- name: Anh N. Tran
  affiliation: Northwestern University, Illinois, USA
  email: trannhatanh89@gmail.com
date: "`r Sys.Date()`"
output: 
    BiocStyle::html_document:
        toc: true
        toc_depth: 2
        toc_float: true
        number_sections: true
vignette: >
  %\VignetteIndexEntry{"6. Tutorial: Download histology images from the Human Protein Atlas"}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

```{r library, message=FALSE, warning=FALSE, error=FALSE}
library(BiocStyle)
library(HPAanalyze)
library(dplyr)
```

# The case 
What to do if you want to systematically download images from HPA?

# The solution

## Get the download links

```{r}
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 ...
```

## Download the images

```{r 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], 
                                    ".jpg"),
                  mode = "wb")
}
```

# Copyright

__Anh Tran, 2018-2021 __

Please cite: __Tran, A.N., Dussaq, A.M., Kennell, T. et al. HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data. BMC Bioinformatics 20, 463 (2019) https://doi.org/10.1186/s12859-019-3059-z __
