inst/doc/z_HPAanalyze_paper_figures.R

In HPAanalyze: Retrieve and analyze data from the Human Protein Atlas

## ----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)
#  library(ggplot2)

## -----------------------------------------------------------------------------
#  data <- hpaDownload(downloadList = "histology",
#                      version = "v18")

## -----------------------------------------------------------------------------
#  gene_list_2 <- c("TP53", "EGFR", "CD44", "PTEN", "IDH1", "IDH2", "CYCS")
#  
#  # Panel 2A
#  tissue_list_2 <- c("skin 1", "cerebellum", "breast")
#  
#  plot_2a <-
#    hpaVisTissue(data = data,
#                 targetGene = gene_list_2,
#                 targetTissue = tissue_list_2,
#                 color = c("#eff3ff", "#bdd7e7","#6baed6", "#2171b5"))
#  
#  ggsave(filename = "plot_2a.pdf",
#         plot = plot_2a,
#         device = "pdf")
#  
#  # Panel 2B
#  cancer_list_2 <- c("breast cancer", "glioma", "lymphoma", "prostate cancer")
#  
#  plot_2b <-
#    hpaVisPatho(data = data,
#                targetGene = gene_list_2,
#                targetCancer = cancer_list_2)
#  
#  ggsave(filename = "plot_2b.pdf",
#         plot = plot_2b,
#         device = "pdf",
#         width = 7,
#         height = 5)
#  
#  # Panel 2C
#  plot_2c <-
#    hpaVisSubcell(data = data,
#                  targetGene = gene_list_2,
#                  color = c("white", "black"),
#                  reliability = c("enhanced", "supported", "approved"))
#  
#  ggsave(filename = "plot_2c.pdf",
#         plot = plot_2c,
#         device = "pdf")

## -----------------------------------------------------------------------------
#  gene_list_3 <-
#    c("GFAP", "EGFR", "PDGFRA", "PIK3CA", "PTEN", "BRAF", "MDM2", "MDM4", "CDK4")
#  
#  # Panel 3A
#  tissue_list_3 <- c("hippocampus", "cerebral cortex")
#  
#  plot_3a <-
#    hpaVisTissue(data = data,
#                 targetGene = gene_list_3,
#                 targetTissue = tissue_list_3,
#                 color = c("#eff3ff", "#bdd7e7","#6baed6", "#2171b5"))
#  
#  ggsave(filename = "plot_3a.pdf",
#         plot = plot_3a,
#         device = "pdf",
#         width = 7,
#         height = 5)
#  
#  # Panel 3B
#  plot_3b <-
#    hpaVisPatho(data = data,
#                targetGene = gene_list_3,
#                targetCancer = "glioma")
#  
#  ggsave(filename = "plot_3b.pdf",
#         plot = plot_3b,
#         device = "pdf",
#         width = 7,
#         height = 5)
#  
#  # Panel 3C
#  gene_list_3c <- c("PTEN", "H3F3A", "DAXX", "PML")
#  
#  plot_3c <-
#    hpaVisSubcell(data = data,
#                  targetGene = gene_list_3c,
#                  color = c("white", "black"),
#                  reliability = c("enhanced", "supported", "approved"))
#  
#  ggsave(filename = "plot_3c.pdf",
#         plot = plot_3c,
#         device = "pdf",
#         width = 4,
#         height = 3)

## -----------------------------------------------------------------------------
#  gene_list_4 <- c("GCH1", "PTS", "SPR", "DHFR")
#  
#  # Panel 4A
#  tissue_list_4 <- c("hippocampus", "cerebral cortex", "caudate")
#  
#  plot_4a <-
#    hpaVisTissue(data = data,
#                 targetGene = gene_list_4,
#                 targetTissue = tissue_list_4,
#                 color = c("#eff3ff", "#bdd7e7","#6baed6", "#2171b5"))
#  
#  ggsave(filename = "plot_4a.pdf",
#         plot = plot_4a,
#         device = "pdf",
#         width = 5,
#         height = 4)
#  
#  # Panel 4B
#  plot_4b <-
#    hpaVisPatho(data = data,
#                targetGene = gene_list_4,
#                targetCancer = "glioma")
#  
#  ggsave(filename = "plot_4b.pdf",
#         plot = plot_4b,
#         device = "pdf",
#         width = 5,
#         height = 4)
#  
#  # Panel 4C
#  # Figure was generated with the GlioVis portal http://gliovis.bioinfo.cnio.es/
#  # Accessed: June 19, 2019
#  #
#  # Plotting:
#  # Navigate through tabs: Explore > Survival > Kaplan-Meier > Plot
#  #
#  # Parameters:
#  #    - Dataset: Adult Rembrandt
#  #    - Gene: SPR or DHFR
#  #    - Histology: All
#  #    - Subtype: All
#  #    - Cutoff: Median
#  #    - Plot options: use default options
#  #    - Download: use default options
#  #
#  # Retrieving plotting data: (same parameters)
#  # Navigate through tabs: Explore > Survival > Kaplan-Meier > Plot
#  # Buttons: Download > CSV
#  
#  # Panel 4D
#  plot_4d <-
#    hpaVisSubcell(data = data,
#                  targetGene = gene_list_4,
#                  color = c("white", "black"),
#                  reliability = c("enhanced", "supported", "approved"))
#  
#  ggsave(filename = "plot_4d.pdf",
#         plot = plot_4d,
#         device = "pdf",
#         width = 4,
#         height = 3)

## -----------------------------------------------------------------------------
#  hpaSubset(data = data,
#            targetGene = "SLC2A3",
#            targetTissue = c("hippocampus", "cerebral cortex", "caudate"),
#            targetCellType = "glial cells",
#            targetCancer = "glioma")
#  
#  # $normal_tissue
#  # # A tibble: 3 x 6
#  #   ensembl         gene   tissue          cell_type   level        reliability
#  #   <chr>           <chr>  <chr>           <chr>       <chr>        <chr>
#  # 1 ENSG00000059804 SLC2A3 caudate         glial cells Not detected Approved
#  # 2 ENSG00000059804 SLC2A3 cerebral cortex glial cells Not detected Approved
#  # 3 ENSG00000059804 SLC2A3 hippocampus     glial cells Not detected Approved
#  #
#  # $pathology
#  # # A tibble: 1 x 11
#  #   ensembl gene  cancer  high medium   low not_detected prognostic_favo~
#  #   <chr>   <chr> <chr>  <dbl>  <dbl> <dbl>        <dbl>            <dbl>
#  # 1 ENSG00~ SLC2~ glioma     1      2     1            8               NA
#  # # ... with 3 more variables: unprognostic_favorable <dbl>,
#  # #   prognostic_unfavorable <dbl>, unprognostic_unfavorable <dbl>
#  #
#  # $subcellular_location
#  # # A tibble: 1 x 11
#  #   ensembl gene  reliability enhanced supported approved uncertain single_cell_var~
#  #   <chr>   <chr> <chr>       <chr>    <chr>     <chr>    <chr>     <chr>
#  # 1 ENSG00~ SLC2~ Approved    NA       NA        Plasma ~ NA        NA
#  # # ... with 3 more variables: single_cell_var_spatial <chr>,
#  # #   cell_cycle_dependency <chr>, go_id <chr>
#  
#  
#  SLC2A3xml <- hpaXmlGet("SLC2A3", version = "v18")
#  
#  SLC2A3_ab <- hpaXmlAntibody(SLC2A3xml)
#  SLC2A3_ab
#  #   id        releaseDate releaseVersion RRID
#  #   <chr>     <chr>       <chr>          <chr>
#  # 1 CAB002763 2006-03-13  1.2            NA
#  # 2 HPA006539 2008-02-15  3.1            AB_1078984
#  
#  SLC2A3_expr <- hpaXmlTissueExpr(SLC2A3xml)
#  str(SLC2A3_expr[[1]])
#  # Classes ‘tbl_df’, ‘tbl’ and 'data.frame':	330 obs. of  18 variables:
#  #  $ patientId         : chr  "2212" "2374" "2068" "2154" ...
#  #  $ age               : chr  "35" "44" "38" "66" ...
#  #  $ sex               : chr  "Male" "Female" "Male" "Female" ...
#  #  $ 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/2763/6778_B_4_5.jpg" "http://v18.proteinatlas.org/images/2763/6778_B_5_5.jpg" "http://v18.proteinatlas.org/images/2763/6778_A_3_2.jpg" "http://v18.proteinatlas.org/images/2763/6778_A_1_2.jpg" ...
#  #  $ snomedCode1       : chr  "M-00100" "M-00100" "M-00100" "M-00100" ...
#  #  $ snomedCode2       : chr  "T-93000" "T-93000" "T-66000" "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" "Appendix" "Appendix" ...
#  #  $ tissueDescription3: chr  NA NA NA NA ...
#  #  $ tissueDescription4: chr  NA NA NA NA ...
#  #  $ tissueDescription5: chr  NA NA NA NA ...
#  
#  dir.create("img")
#  
#  SLC2A3_norm <-
#    SLC2A3_expr[[1]] %>%
#    filter(tissueDescription1 == "Normal tissue, NOS") %>%
#    filter(tissueDescription2 %in% c("Cerebral cortex", "Hippocampus", "Lateral ventricle wall"))
#  
#  for (i in 1:nrow(SLC2A3_norm)) {
#      download.file(SLC2A3_norm$imageUrl[i],
#                    destfile = paste0("img/", SLC2A3_ab$id[1], "_",
#                                      SLC2A3_norm$patientId[i], "_",
#                                      SLC2A3_norm$tissueDescription2[i], "_",
#                                      SLC2A3_norm$staining[i],
#                                      ".jpg"),
#                    mode = "wb")
#  }
#  
#  SLC2A3_glioma <-
#    SLC2A3_expr[[1]] %>%
#    filter(tissueDescription1 %in% c("Glioma, malignant, High grade", "Glioma, malignant, Low grade", "Glioma, malignant, NOS"))
#  
#  for (i in 1:nrow(SLC2A3_glioma)) {
#      download.file(SLC2A3_glioma$imageUrl[i],
#                    destfile = paste0("img/", SLC2A3_ab$id[1], "_",
#                                      SLC2A3_glioma$patientId[i], "_",
#                                      SLC2A3_glioma$tissueDescription1[i], "_",
#                                      SLC2A3_glioma$staining[i],
#                                      ".jpg"),
#                    mode = "wb")
#  }