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 = NULL, targetGene = NULL, targetTissue = NULL,
      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. Use HPA version 18 by default.
`targetGene` | Vector of strings of HGNC gene symbols. By default it is set to `c('TP53', 'EGFR', 'CD44', 'PTEN', 'IDH1')`. You can also mix HGNC gene symbols and ensemnl ids (start with ENSG) and they will be converted to HGNC gene symbols.
`targetTissue` | Vector of strings of normal tissues. Default to breast.
`targetCellType` | Vector of strings of normal cell types. Default to all.
`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.

### See Also

Other visualization functions: `hpaVisPatho`, `hpaVisSubcell`, `hpaVis`

### 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)

[Package HPAanalyze version 1.2.1 Index]