plot_pca {MultiBaC} | R Documentation |
plot_pca
plot_pca(mbac, col.by.batch = TRUE, col.per.group = NULL, comp2plot = c(1, 2), typeP = "pca.both", legend.text = NULL, args.legend = NULL, ...)
mbac |
Object of class mbac generated by *createMbac*, *ARSyNbac*, *MultiBaC*, *genModelList*, or *batchCorrection*. |
col.by.batch |
Argument for PCA plots. TRUE or FALSE. If TRUE (default) samples are gruped according to the batch factor. If FALSE samples are gruped according to the experimental desing. |
col.per.group |
Argument for PCA plot. Indicates the color for each group defined in "groups" argument. If NULL (default) the colors are taken from a predefined pallete. |
comp2plot |
Indicates which components are plotted. Default is "c(1,2)", which means that component 1 is plotted in "x" axis and component 2 in "y" axis. If more components are indicated, the function will return as many plots as needed to show all the components. |
typeP |
"pca.cor", "pca.org" or "pca.both". If inputOmics contains original matrices, set "pca.org". However, if inputOmics contains the corrected matrices, set "pca.cor". |
legend.text |
a vector of text used to construct a legend for the plot. |
args.legend |
list of additional arguments to pass to legend(); names of the list are used as argument names. Only used if legend.text is supplied. |
... |
Other graphical arguments. |
A PCA plot is displayed.
data('multiyeast') my_mbac <- createMbac (inputOmics = list(A.rna, A.gro, B.rna, B.ribo, C.rna, C.par), batchFactor = c("A", "A", "B", "B", "C", "C"), experimentalDesign = list("A" = c("Glu+", "Glu+", "Glu+", "Glu-", "Glu-", "Glu-"), "B" = c("Glu+", "Glu+", "Glu-", "Glu-"), "C" = c("Glu+", "Glu+", "Glu-", "Glu-")), omicNames = c("RNA", "GRO", "RNA", "RIBO", "RNA", "PAR")) plot_pca(my_mbac, typeP = "pca.org") my_final_mbac <- MultiBaC (my_mbac, test.comp = NULL, scale = FALSE, center = TRUE, crossval = NULL, Variability = 0.90, Interaction = TRUE , showplot = FALSE, showinfo = FALSE) plot_pca(my_final_mbac, typeP = "pca.cor")