## ----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 # #> # #> 1 CAB000115 2006-03-13 1.2 # #> 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") # }