Generate expression heatmap

A function for generating a heat map of marker expression across clusters

Usage

markerHeatmap(
  data,
  markers = NULL,
  clusters = NULL,
  threshold = 2,
  clusterMarkers = FALSE,
  fontSize = 14
)

Arguments

data

a matrix or dataframe where the rows are samples and columns are markers

markers

a list of markers of interest. If not provided, all columns will be used

clusters

a vector of cluster labels

threshold

the value to threshold the marker expression at

clusterMarkers

should the rows(markers) of the heatmap be clustered

fontSize

the size of the text on the heatmap

Value

a heatmap with the markers in the rows and clusters in the columns

Author

Elijah WIllie ewil3501@uni.sydney.edu.au

Examples

data("risom_dat")
risomMarkers <- c(
  "CD45", "SMA", "CK7", "CK5", "VIM", "CD31", "PanKRT", "ECAD"
)
res <- runFuseSOM(risom_dat, markers = risomMarkers, numClusters = 23)
#> You have provided a dataset of class data.frame
#> Everything looks good. Now running the FuseSOM algorithm
#> Now Generating the Self Organizing Map Grid
#> Optimal Grid Size is: 5
#> Now Running the Self Organizing Map Model
#> Now Clustering the Prototypes
#> Now Mapping Clusters to the Original Data
#> The Prototypes have been Clustered and Mapped Successfully
#> The FuseSOM algorithm has completed successfully
p.heat <- markerHeatmap(risom_dat, risomMarkers, clusters = res$clusters)