hpaVisTissue {HPAanalyze} | R Documentation |
Visualize the expression of protein of interest in each target tissue by cell types.
hpaVisTissue(data, targetGene, targetTissue, targetCellType = NULL, color = c("#ffffb2", "#fecc5c", "#fd8d3c", "#e31a1c"), customTheme = FALSE)
data |
Input the list object generated by |
targetGene |
Vector of strings of HGNC gene symbols. |
targetTissue |
Vector of strings of normal tissues. |
targetCellType |
Vector of strings of normal cell types. |
color |
Vector of 4 colors used to depict different expression levels. |
customTheme |
Logical argument. If |
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.
Other visualization functions: hpaVisPatho
,
hpaVisSubcell
, hpaVis
data("hpa_downloaded_histology_v18") geneList <- c('TP53', 'EGFR', 'CD44', 'PTEN', 'IDH1', 'IDH2', 'CYCS') tissueList <- c('breast', 'cerebellum', 'skin 1') ## A typical function call hpaVisTissue(data=hpa_downloaded_histology_v18, targetGene=geneList, targetTissue=tissueList)