dimensionReductionPlot: Plot the coordinates from 'dimensionReduction' values

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

Plot the coordinates from dimensionReduction values

Description

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

Usage

dimensionReductionPlot(
  tbl,
  se,
  color = c("none", colnames(se@colData)),
  size = c("none", colnames(se@colData)),
  explainedVar = NULL,
  x_coord,
  y_coord,
  height = 600,
  interactive = TRUE
)

Arguments

tbl	tbl as obtained by the function dimensionReduction
se	SummarizedExperiment
color	character, one of "none" or colnames(se@colData)
size	character, one of "none" or colnames(se@colData)
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)
interactive	logical(1), if TRUE dimensionReductionPlot will return a plotly object, if FALSE dimensionReductionPlot will return a gg object

Details

The function dimensionReductionPlot is a wrapper for a ggplot/ggplotly expression.

Value

plotly or gg

Author(s)

Thomas Naake

Examples

library(SummarizedExperiment)

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

pca <- dimensionReduction(x = assay(se), type = "PCA", params = list())[[1]]

dimensionReductionPlot(tbl = pca, se = se, color = "type", size = "median_vals",
    x_coord = "PC1", y_coord = "PC2")

tnaake/MatrixQCvis documentation built on Nov. 4, 2024, 7:42 a.m.