hpaVis: Visualize data in one function

In HPAanalyze: Retrieve and analyze data from the Human Protein Atlas

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.
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()

HPAanalyze documentation built on Nov. 26, 2020, 2:01 a.m.