hpaVisSubcell {HPAanalyze}R Documentation

Visualize subcellular location data

Description

Visualize the the confirmed subcellular locations of genes of interest.

Usage

hpaVisSubcell(data, targetGene, color = c("#ffffb2", "#e31a1c"),
  customTheme = FALSE)

Arguments

data

Input the list object generated by hpa_download() or hpa_subset(). Require the subcellular_location dataset.

targetGene

Vector of strings of HGNC gene symbols.

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 1.0.0 Index]