hpaVisSubcell: Visualize subcellular location data
In HPAanalyze: Retrieve and analyze data from the Human Protein Atlas

Description Usage Arguments Value See Also Examples

Visualize the the confirmed subcellular locations of genes of interest.

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

`data`	Input the list object generated by `hpa_download()` or `hpa_subset()`. Require the `subcellular_location` dataset. Use HPA histology data (built-in) 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.

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.

Other visualization functions: hpaVisPatho(), hpaVisTissue(), hpaVis()

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

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