hpaVisSubcell {HPAanalyze} | R Documentation

## Visualize subcellular location data

### Description

Visualize the the confirmed subcellular locations of genes of interest.

### Usage

    hpaVisSubcell(data = NULL, targetGene = NULL,
      reliability = c("enhanced", "supported", "approved", "uncertain"),
      color = c("#ffffb2", "#e31a1c"), customTheme = FALSE)

### Arguments

`data` | Input the list object generated by `hpa_download()` or `hpa_subset()`. Require the `subcellular_location` 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.
`reliability` | Vector of string indicate which reliability scores you want to plot. The default is everything `c("enhanced", "supported", "approved", "uncertain")`.
`color` | Vector of 2 colors used to depict if the protein expresses in a location or not.
`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 subcellular location data is visualized as a tile graph, in which the x axis includes the inquired proteins and the y axis contain the subcellular locations.

### See Also

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

### Examples

      data("hpa_downloaded_histology_v18")
      geneList <- c('TP53', 'EGFR', 'CD44', 'PTEN', 'IDH1', 'IDH2', 'CYCS')

      ## A typical function call
      hpaVisSubcell(data=hpa_downloaded_histology_v18,
                      targetGene=geneList)

[Package HPAanalyze version 1.2.1 Index]