modpcomp | R Documentation |
extract module pca component
modpcomp(data, colors, nPC = 2, plot = FALSE, filename = NULL, group = NULL)
data |
protein quantification data. column is sample. row is protein ID. |
colors |
protein and module information. which is calculated in WGCNA package. |
nPC |
how many PCA component will saved. |
plot |
a logical value indicating whether draw PCA plot. This function need load ggfortify first. |
filename |
The filename of plot. The default value is |
group |
sample group information. |
Kefu Liu
data(net) data(imputedData) data <- imputedData logD <- data$log2_value rownames(logD) <- data$inf$ori.ID Module_PCA <- modpcomp(logD, net$colors) # if plot PCA and plot module 6 PCA group <- gsub("[0-9]+", "", colnames(logD)) pos <- which(net$colors == 6) if (requireNamespace("ggfortify", quietly = TRUE)){ require("ggfortify") Module_PCA <- modpcomp(logD[pos,], net$colors[pos], plot = TRUE, group = group) }
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