This function takes as input an scToolkit object. It creates a multidimensional scaling plot to vizualise global similarity between samples using the median marker expression across all cells in each channel for each sample. It uses the metadata "group" slot to split the expression data into each individual sample. It also takes as input an optional "feature" metadata slot to color the plot by this feature, for instance to display an experimental condition overlayed on the samples. I have attached the two versions of output on some cytof data I have as example. Plotting is done in ggplot2 and the mds plot funciton is taken from the limma package.
This function takes as input an scToolkit object. It creates a multidimensional scaling plot to vizualise global similarity between samples using the median marker expression across all cells in each channel for each sample. It uses the metadata "group" slot to split the expression data into each individual sample. It also takes as input an optional "feature" metadata slot to color the plot by this feature, for instance to display an experimental condition overlayed on the samples. I have attached the two versions of output on some cytof data I have as example. Plotting is done in ggplot2 and the mds plot funciton is taken from the limma package.