plotPCALoadings {MatrixQCvis}R Documentation

Plot for PCA loadings of features

Description

The function 'plotPCALoadings' creates a loadings plot of the features.

Usage

plotPCALoadings(tbl, x_coord, y_coord)

Arguments

tbl

'tbl' as obtained by the function 'ordination'

x_coord

'character', column name of 'tbl' that stores x coordinates

y_coord

'character', column name of 'tbl' that stores y coordinates

Details

The function takes as input the output of the function 'tblPlotPCALoadings'. It uses the 'ggplotly' function from 'plotly' to create an interactive 'plotly' plot.

Value

'plotly'

Author(s)

Thomas Naake

Examples

x <- matrix(rnorm(1:10000), ncol = 100)
rownames(x) <- paste("feature", 1:nrow(x))
colnames(x) <- paste("sample", 1:ncol(x))
params <- list(method = "euclidean", ## dist
    initial_dims = 10, max_iter = 100, dims = 3, perplexity = 3, ## tSNE
    min_dist = 0.1, n_neighbors = 15, spread = 1) ## UMAP
tbl <- tblPCALoadings(x, params)
plotPCALoadings(tbl, x_coord = "PC1", y_coord = "PC2")


[Package MatrixQCvis version 1.0.0 Index]