--- title: "99. Code for figures from HPAanalyze paper" author: - name: Anh N. Tran affiliation: DataGrata LLC email: trannhatanh89@gmail.com date: 6/18/2019 output: BiocStyle::html_document: toc: true toc_depth: 2 toc_float: true number_sections: true vignette: > %\VignetteIndexEntry{"99. Code for figures from HPAanalyze paper"} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- ```{r setup, include=FALSE} knitr::opts_chunk$set( collapse=TRUE, comment="#>", warning=FALSE, error=FALSE, eval=FALSE ) ``` ```{r library, message=FALSE, warning=FALSE, error=FALSE} library(BiocStyle) library(HPAanalyze) library(dplyr) library(ggplot2) ``` ```{r} 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. # Figure 2 ```{r} 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") ``` # Figure 3 ```{r} 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) ``` # Figure 4 ```{r} 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) ``` # Figure 5 ```{r} 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 # # 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~ # # 1 ENSG00~ SLC2~ glioma 1 2 1 8 NA # # ... with 3 more variables: unprognostic_favorable , # # prognostic_unfavorable , unprognostic_unfavorable # # $subcellular_location # # A tibble: 1 x 11 # ensembl gene reliability enhanced supported approved uncertain single_cell_var~ # # 1 ENSG00~ SLC2~ Approved NA NA Plasma ~ NA NA # # ... with 3 more variables: single_cell_var_spatial , # # cell_cycle_dependency , go_id SLC2A3xml <- hpaXmlGet("SLC2A3", version = "v18") SLC2A3_ab <- hpaXmlAntibody(SLC2A3xml) SLC2A3_ab # id releaseDate releaseVersion RRID # # 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") } ``` # Copyright __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 __