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Visualize tissue data

Source: R/vis.R
hpaVisTissue.Rd

Visualize the expression of protein of interest in each target tissue by cell types.

Usage

hpaVisTissue(
  data = NULL,
  targetGene = NULL,
  targetTissue = NULL,
  targetCellType = NULL,
  color = c("#FCFDBF", "#FE9F6D", "#DE4968", "#8C2981"),
  customTheme = FALSE
)

Arguments

data

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

targetTissue

Vector of strings of normal tissues. Default to all.

targetCellType

Vector of strings of normal cell types. Default to all.

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.

Value

This function will return a ggplot2 plot object, which can be further modified if desirable. The tissue data is visualized as a heatmap: x axis contains inquired protein and y axis contains tissue/cells of interest.

See also

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

Examples

  data("hpa_histology_data")
  geneList <- c('TP53', 'EGFR', 'CD44', 'PTEN', 'IDH1', 'IDH2', 'CYCS')
  tissueList <- c('breast', 'cerebellum', 'skin 1')

  ## A typical function call
  hpaVisTissue(data=hpa_histology_data,
               targetGene=geneList,
               targetTissue=tissueList)
#> * WARNING: targetCellType variable not specified, visualize all.
#> >> Use hpaListParam() to list possible values for target variables.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.