## ----setup, include=FALSE-------------------------------------------------- knitr::opts_chunk$set( collapse=TRUE, comment="#>", warning=FALSE, message=FALSE, error=FALSE ) ## ----library--------------------------------------------------------------- library(BiocStyle) library(HPAanalyze) library(tibble) library(dplyr) library(ggplot2) library(hpar) ## ----downloadedData, eval=FALSE-------------------------------------------- # downloadedData <- hpaDownload(downloadList='all') # summary(downloadedData) # # #> Length Class Mode # #> normal_tissue 6 tbl_df list # #> pathology 11 tbl_df list # #> subcellular_location 11 tbl_df list # #> rna_tissue 5 tbl_df list # #> rna_cell_line 5 tbl_df list # #> transcript_rna_tissue 4 tbl_df list # #> transcript_rna_cell_line 4 tbl_df list ## ----normal_tissue--------------------------------------------------------- downloadedData <- hpaDownload(downloadList='histology', version='example') tibble::glimpse(downloadedData$normal_tissue, give.attr=FALSE) ## ----pathology------------------------------------------------------------- tibble::glimpse(downloadedData$pathology, give.attr=FALSE) ## ----subcellular_location-------------------------------------------------- tibble::glimpse(downloadedData$subcellular_location, give.attr=FALSE) ## ----rna1, warning=FALSE, message=FALSE------------------------------------ downloadedData <- hpaDownload(downloadList='rna', version='hpar') tibble::glimpse(downloadedData$rna_tissue, give.attr=FALSE) ## ----rna2, warning=FALSE, message=FALSE------------------------------------ tibble::glimpse(downloadedData$rna_cell_line, give.attr=FALSE) ## ----isoform1, eval=FALSE-------------------------------------------------- # downloadedData <- hpaDownload(downloadList='isoform', version='v18') # # tibble::glimpse(downloadedData$transcript_rna_tissue, give.attr=FALSE) # # #> Observations: 27,535,996 # #> Variables: 4 # #> $ ensembl "ENSG00000000003", "ENSG00000000003", "ENSG0000000... # #> $ transcript "ENST00000373020", "ENST00000494424", "ENST0000049... # #> $ tissue "adipose tissue.V1", "adipose tissue.V1", "adipose... # #> $ value 27.3577003, 0.0000000, 1.9341500, 1.6059300, 0.000... ## ----isoform2, eval=FALSE-------------------------------------------------- # tibble::glimpse(downloadedData$transcript_rna_cell_line, give.attr=FALSE) # # #> Observations: 20,972,183 # #> Variables: 4 # #> $ ensembl "ENSG00000000003", "ENSG00000000003", "ENSG0000000... # #> $ transcript "ENST00000373020", "ENST00000494424", "ENST0000049... # #> $ cell_line "A-431.C35", "A-431.C35", "A-431.C35", "A-431.C35"... # #> $ value 29.406799, 0.000000, 0.992916, 0.398387, 0.239204,... ## ----hpar1, eval=FALSE----------------------------------------------------- # hpaDownload('all', 'hpar') ## ----hpar2----------------------------------------------------------------- hpar::getHpaVersion() hpar::getHpaDate() hpar::getHpaEnsembl() ## ----list_param, eval=FALSE------------------------------------------------ # downloadedData <- hpaDownload(downloadList='all') # str(hpaListParam(downloadedData)) # # #> List of 6 # #> $ normal_tissue : chr [1:58] "adrenal gland" "appendix" "bone marrow" "breast" ... # #> $ normal_cell : chr [1:82] "glandular cells" "lymphoid tissue" "hematopoietic cells" "adipocytes" ... # #> $ cancer : chr [1:20] "breast cancer" "carcinoid" "cervical cancer" "colorectal cancer" ... # #> $ subcellular_location: chr [1:32] "Cytosol" "Mitochondria" "Aggresome" "Plasma membrane" ... # #> $ normal_tissue_rna : chr [1:37] "adipose tissue" "adrenal gland" "appendix" "bone marrow" ... # #> $ cell_line_rna : chr [1:64] "A-431" "A549" "AF22" "AN3-CA" ... ## ----subset1, message=FALSE, warning=FALSE--------------------------------- downloadedData <- hpaDownload(downloadList='histology', version='example') sapply(downloadedData, nrow) ## ----subset2, message=FALSE, warning=FALSE--------------------------------- geneList <- c('TP53', 'EGFR', 'CD44', 'PTEN', 'IDH1', 'IDH2', 'CYCS') tissueList <- c('breast', 'cerebellum', 'skin 1') cancerList <- c('breast cancer', 'glioma', 'melanoma') cellLineList <- c('A-431', 'A549', 'AF22', 'AN3-CA') subsetData <- hpaSubset(data=downloadedData, targetGene=geneList, targetTissue=tissueList, targetCancer=cancerList, targetCellLine=cellLineList) sapply(subsetData, nrow) ## -------------------------------------------------------------------------- id <- c("ENSG00000000003", "ENSG00000000005") hpar::getHpa(id, hpadata="hpaNormalTissue") %>% tibble::glimpse() ## ----eval=FALSE------------------------------------------------------------ # hpaExport(subsetData, fileName='subset.xlsx', fileType='xlsx') ## ----visData, echo=FALSE, warning=FALSE, message=FALSE--------------------- downloadedData <- hpaDownload('histology', 'example') ## ----visTissue, fig.wide--------------------------------------------------- geneList <- c('TP53', 'EGFR', 'CD44', 'PTEN', 'IDH1', 'IDH2', 'CYCS') tissueList <- c('breast', 'cerebellum', 'skin 1') hpaVisTissue(downloadedData, targetGene=geneList, targetTissue=tissueList) ## ----visPatho, fig.wide---------------------------------------------------- geneList <- c('TP53', 'EGFR', 'CD44', 'PTEN', 'IDH1', 'IDH2', 'CYCS') cancerList <- c('breast cancer', 'glioma', 'lymphoma', 'prostate cancer') colorGray <- c('slategray1', 'slategray2', 'slategray3', 'slategray4') hpaVisPatho(downloadedData, targetGene=geneList, targetCancer=cancerList, color=colorGray) ## ----visSubcell------------------------------------------------------------ geneList <- c('TP53', 'EGFR', 'CD44', 'PTEN', 'IDH1', 'IDH2', 'CYCS') hpaVisSubcell(downloadedData, targetGene=geneList, customTheme=TRUE) + ggplot2::theme_minimal() + ggplot2::ylab('Subcellular locations') + ggplot2::xlab('Protein') + ggplot2::theme(axis.text.x=element_text(angle=45, hjust=1)) + ggplot2::theme(legend.position="none") + ggplot2::coord_equal() ## ----XmlGet---------------------------------------------------------------- CCNB1xml <- hpaXmlGet('ENSG00000134057') ## ----hpar_site, eval=FALSE------------------------------------------------- # hpar::getHpa('ENSG00000134057', type="details") ## ----XmlProtClass---------------------------------------------------------- hpaXmlProtClass(CCNB1xml) ## ----XmlTissueExprSum------------------------------------------------------ hpaXmlTissueExprSum(CCNB1xml) ## ----XmlAntibody----------------------------------------------------------- hpaXmlAntibody(CCNB1xml) ## ----XmlTissueExpr1-------------------------------------------------------- tissueExpression <- hpaXmlTissueExpr(CCNB1xml) summary(tissueExpression) ## ----XmlTissueExpr2-------------------------------------------------------- tissueExpression[[1]] ## ----echo=FALSE------------------------------------------------------------ sessionInfo()