DaMiR.Allplot {DaMiRseq} | R Documentation |
This is a helper function to easily draw (1) clustering dendrogram and heatmap of a sample-per-sample correlation matrix, (2) multidimensional scaling plots (MDS), (3) relative log expression (RLE) boxplots of expression data, (4) a sample-by-sample expression value distribution, and (5) a class average expression value distribution
DaMiR.Allplot(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 and known variables (or a subset of them); at least one column with 'class' label must be included |
type |
A character string specifing the metric to be applied to correlation analysis. Either "spearman" or "pearson" is allowed; default is "spearman" |
Please be sure that NAs are not present in df
's columns.
Plots will not be drawn in the presence of NAs.
A dendrogram and heatmap, MDS plot(s), a RLE boxplot, a sample-by-sample expression value distribution, and a class average expression value distribution
Mattia Chiesa, Luca Piacentini
# use example data: data(data_norm) data(df) # Draw clustering dendrogram and heatmap, MDS, RLE boxplot: DaMiR.Allplot(data=data_norm, df=df[,5,drop=FALSE])