plotPCALoadings: Plot for PCA loadings of features

In tnaake/MatrixQCvis: Shiny-based interactive data-quality exploration for omics data

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 dimensionReduction
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(seq_len(10000)), ncol = 100)
rownames(x) <- paste("feature", seq_len(nrow(x)))
colnames(x) <- paste("sample", seq_len(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")

tnaake/MatrixQCvis documentation built on June 20, 2024, 7:22 a.m.