DaMiR.MDSplot {DaMiRseq} | R Documentation |
A MDS plot is drawn in order to visualize class clustering.
DaMiR.MDSplot(data, df, type = c("spearman", "pearson"))
data |
A SummarizedExperiment object or a matrix or a data.frame where rows and cols should be, respectively, observations and features |
df |
A data frame with class; it can be directly subset from data |
type |
A character string specifing the metric to be applied to correlation analysis. Either "spearman" or "pearson" is allowed; default is "spearman" |
The MDS plot is drawn taking as input a dissimilarity matrix produced by either a sample-per-sample Pearson's or Spearman's correlation of normalized expression data.
A MDS plot, using only 'class' information
Mattia Chiesa, Luca Piacentini
# use example data: data(data_reduced) data(df) # Draw MDS: DaMiR.MDSplot(data=data_reduced, df=df, type="pearson")