R: Visualize tissue data

hpaVisTissue {HPAanalyze}

R Documentation

Visualize tissue data

Description

Visualize the expression of protein of interest in each target tissue by cell types.

Usage

hpaVisTissue(data, targetGene, targetTissue, targetCellType = NULL,
  color = c("#ffffb2", "#fecc5c", "#fd8d3c", "#e31a1c"),
  customTheme = FALSE)

Arguments

`data`	Input the list object generated by `hpa_download()` or `hpa_subset()`. Require the `normal_tissue` dataset.
`targetGene`	Vector of strings of HGNC gene symbols.
`targetTissue`	Vector of strings of normal tissues.
`targetCellType`	Vector of strings of normal cell types.
`color`	Vector of 4 colors used to depict different expression levels.
`customTheme`	Logical argument. If `TRUE`, the function will return a barebone ggplot2 plot to be customized further.

Value

This function will return a ggplot2 plot object, which can be further modified if desirable. The tissue data is visualized as a heatmap: x axis contains inquired protein and y axis contains tissue/cells of interest.

Examples

  data("hpa_downloaded_histology_v18")
  geneList <- c('TP53', 'EGFR', 'CD44', 'PTEN', 'IDH1', 'IDH2', 'CYCS')
  tissueList <- c('breast', 'cerebellum', 'skin 1')

  ## A typical function call
  hpaVisTissue(data=hpa_downloaded_histology_v18,
               targetGene=geneList,
               targetTissue=tissueList)