--- title: "99. Code for figures from HPAanalyze paper" author: - name: Anh N. Tran affiliation: Northwestern University, Illinois, USA 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") ``` # 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 ```{r child = 'data/copyright', eval = TRUE} ```