knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.align = "center" )
Firstly, assume you have already installed UCSCXenaShiny package.
library(UCSCXenaShiny)
From UCSCXenaShiny v2, we provide a comprehensive tutorial book for introducing how to use the datasets, functions, and the Shiny application.
We provide function to retrieve multi-dimensional data including genomic, epigenomic, transcriptomic, and proteomic data from TCGA (note, this actually contains data from TCGA/TARGET/GTEx databases) and CCLE Pan-Cancer dataset for single identifier (e.g., gene, protein).
Check parameters:
args(query_pancan_value)
For TCGA gene expression data, we use Xena dataset with ID TcgaTargetGtex_rsem_gene_tpm
which includes 19131 samples with tumor tissue samples and normal tissue samples. The expression value unit is log2(tpm+0.001)
.
Let's check several examples.
gene_expr <- query_pancan_value("TP53")
str(gene_expr)
transcript_expr <- query_pancan_value("ENST00000000233", data_type = "transcript")
gene_cnv <- query_pancan_value("TP53", data_type = "cnv")
gene_mut <- query_pancan_value("TP53", data_type = "mutation")
miRNA_expr <- query_pancan_value("hsa-let-7a-2-3p", data_type = "miRNA")
vis_toil_TvsN(Gene = "TP53", Mode = "Violinplot", Show.P.value = FALSE, Show.P.label = FALSE)
vis_toil_TvsN_cancer( Gene = "TP53", Mode = "Violinplot", Show.P.value = TRUE, Show.P.label = TRUE, Method = "wilcox.test", values = c("#DF2020", "#DDDF21"), TCGA.only = FALSE, Cancer = "ACC" )
This function needs gganatogram package, which is not on CRAN. Please install it before using this function.
if (require("gganatogram")) { vis_pancan_anatomy(Gene = "TP53", Gender = c("Female", "Male"), option = "D") }
vis_unicox_tree( Gene = "TP53", measure = "OS", threshold = 0.5, values = c("grey", "#E31A1C", "#377DB8") )
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