densityPlot {MetaCyto} | R Documentation |
A function that draws density plot for each cell cluster.
densityPlot(fcsFrame, clusterList, cutoff, markerToPlot = NULL)
fcsFrame |
A flow Frame object returned from preprocessing function. |
clusterList |
A list, each element should be a vector containing the IDs of all cells that belong to a cluster |
cutoff |
A vector of cutoff values to bisect the distribution of each marker. The names of the vector should be the same as the marker names. |
markerToPlot |
A vector specifying markers included in the plot. If NULL, all markers will be plotted. |
The plot can be very large, we suggest plotting it into a pdf jpeg file directly.
NULL. The plot will show up automatically.
# Find fcs files files=system.file("extdata","SDY420/ResultFiles/CyTOF_result", package="MetaCyto") files=list.files(files,pattern="fcs$",full.names=TRUE) # Preprocess fcs = preprocessing(fcsFiles=files,assay ="CyTOF",b=1/8) # Search clusters cluster_list=searchCluster(fcsFrame=fcs, clusterLabel=c("CD3+|CD8+","CD3-|CD19+")) # plot density plot for clusters densityPlot(fcs, clusterList=cluster_list$clusterList, cutoff=cluster_list$cutoff, markerToPlot=c("CD3","CD8","CD19"))