PlotDimRed {FlowSOM} | R Documentation |
Plot a dimensionality reduction
PlotDimRed( fsom, colsToUse = fsom$map$colsUsed, colorBy = "metaclusters", cTotal = NULL, dimred = Rtsne::Rtsne, extractLayout = function(dimred) { dimred$Y }, label = TRUE, returnLayout = FALSE, seed = NULL, title = NULL, ... )
fsom |
FlowSOM object, as generated by |
colsToUse |
The columns used for the dimensionality reduction. Default = fsom$map$colsUsed. |
colorBy |
Defines how the dimensionality reduction will be colored. Can be "metaclusters" (default), "clusters" or a marker/channel/index. |
cTotal |
The total amount of cells to be used in the dimensionality reduction. Default is all the cells. |
dimred |
A dimensionality reduction function. Default = Rtsne::Rtsne. Alternatively, a data.frame or matrix with either equal number of rows to the fsom or an OriginalID column. Recommended to put cTotal to NULL when providing a matrix (or ensuring that the dimred corresponds to subsampling the flowSOM data for cTotal cells with the same seed). |
extractLayout |
A function to extract the coordinates from the results of the dimred default = function(dimred)dimred$Y. |
label |
If label = TRUE (default), labels are added to plot. |
returnLayout |
If TRUE, this function returns a dataframe with the layout of dimred and the original IDs and the plot. Default = FALSE. |
seed |
A seed for reproducibility. |
title |
A title for the plot. |
... |
Additional arguments to pass to dimred. |
Plot a dimensionality reduction of fsom$data
A dimensionality reduction plot made in ggplot2
file <- system.file("extdata", "68983.fcs", package="FlowSOM") flowSOM.res <- FlowSOM(file, compensate = TRUE, transform = TRUE, scale = TRUE, colsToUse = c(9, 12, 14:18), nClus = 10, silent = FALSE, xdim = 7, ydim = 7) PlotDimRed(flowSOM.res, cTotal = 5000, seed = 1, title = "t-SNE") PlotDimRed(flowSOM.res, cTotal = 5000, colorBy = "CD3", seed = 1, title = "t-SNE")