ordinationPlot {MatrixQCvis}R Documentation

Plot the coordinates from 'ordination' values

Description

The function 'ordinationPlot' creates a dimension reduction plot. The function takes as input the 'tbl' object obtained from the 'ordination' function. The 'tbl' contains transformed values by one of the ordination methods.

Usage

ordinationPlot(
  tbl,
  se,
  highlight = c("none", colnames(colData(se))),
  explainedVar = NULL,
  x_coord,
  y_coord,
  height = 600
)

Arguments

tbl

'tbl' as obtained by the function 'ordination'

se

'SummarizedExperiment'

highlight

'character', one of '"none"' or 'colnames(colData(se))'

explainedVar

NULL or named 'numeric', if 'numeric' 'explainedVar' contains the explained variance per principal component (names of 'explainedVar' corresponds to the principal components)

x_coord

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

y_coord

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

height

'numeric', specifying the height of the plot (in pixels)

Details

The function 'ordinationPlot' is a wrapper for a 'ggplot'/'ggplotly' expression.

Value

'plotly'

Author(s)

Thomas Naake

Examples

library(SummarizedExperiment)

## create se
a <- matrix(1:100, nrow = 10, ncol = 10, byrow = TRUE,
            dimnames = list(1:10, paste("sample", 1:10)))
set.seed(1)
a <- a + rnorm(100)
cD <- data.frame(name = colnames(a), type = c(rep("1", 5), rep("2", 5)))
rD <- data.frame(spectra = rownames(a))
se <- SummarizedExperiment(assay = a, rowData = rD, colData = cD)

pca <- ordination(x = assay(se), type = "PCA", params = list())

ordinationPlot(tbl = pca, se = se, highlight = "type", 
    x_coord = "PC1", y_coord = "PC2")


[Package MatrixQCvis version 1.1.2 Index]