library(BiocStyle)
library(HPAanalyze)
library(dplyr)
library(ggplot2)data <- hpaDownload(downloadList = "histology",
version = "v18")This code will only work with the version of HPAanalyze that is used to generate the figures in the paper. Due to subsequent updates to the package, the code may not work with the latest version of HPAanalyze.
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")
}Anh Tran, 2018-2025
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