hpaVis {HPAanalyze} | R Documentation

## Visualize data in one function

### Description

This function is an universal visualization function that allow calling other hpaVis functions via a single function call. By default, this function will use the dataset bundled with HPAanalyze, and provide a grid of all available plots. The types of plots in the output can be specified via the `visType` argument. If only one plot type is specified, this function will return the exact same output as the specific hpaVis function used to create the plot.

### Usage

    hpaVis(data = NULL, targetGene = NULL, targetTissue = NULL,
      targetCellType = NULL, targetCancer = NULL, visType = c("Tissue",
      "Patho", "Subcell"), color = c("#ffffb2", "#fecc5c", "#fd8d3c",
      "#e31a1c"), customTheme = FALSE, ...)

### Arguments

`data` | Input the list object generated by `hpa_download()` or `hpa_subset()`. By default this function use the example dataset bundled with HPAanalyze, which is from version 18 of the HPA program.
`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 tissue names. By default it is set to `"breast"`.
`targetCellType` | Vector of strings of normal cell types. By default inludes all available cell types in the target tissues.
`targetCancer` | Vector of strings of normal tissues. By default it is set to `"breast cancer"`.
`visType` | Vector of strings indicating which plots will be generated. Currently available values are `"all"`, `"Tissue"`, `"Patho"`, `"Cancer"`, `"Subcell"`.
`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.
`...` | Additional arguments to be passed downstream to other hpaVis functions being called behind the scene. These arguments includes `targetTissue`, `targetCellType`, `targetCancer`. See documentation for individual hpaVis functions for more information.

### Value

If multiple visType is chosen, this function will return multiple graphs in one panel. If only one visType is chosen, this function will return a ggplot2 plot object, which can be further modified if desirable. See help file for each of the hpaVis function for more information about individual graphs.

### See Also

`hpaDownload`, `hpaSubset`

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

### Examples

      hpaVis()

[Package HPAanalyze version 1.2.1 Index]