Visualize subcellular location data

Source: R/vis.R

Visualize the the confirmed subcellular locations of genes of interest.

hpaVisSubcell(
  data = NULL,
  targetGene = NULL,
  reliability = c("enhanced", "supported", "approved", "uncertain"),
  color = c("#FCFDBF", "#8C2981"),
  customTheme = FALSE
)

Arguments

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

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