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findTopGenes

Source: R/findTopGenes.R
findTopGenes.Rd

A function to find and visualise the genes with the highest (in absolute value) loading in WSIR1. These genes contribute the most to the first low-dimensional direction.

Usage

findTopGenes(WSIR, highest = 10, dirs = 1)

Arguments

WSIR

wsir object as output of wSIR function. To analyse a different DR method, ensure the slot named 'directions' contains the loadings as a matrix with the gene names as the rownames.

highest

integer for how many of the top genes you would like to see. Recommend no more than 20 for ease of visualisation. Default is 10.

dirs

integer or vector for which direction / directions you want to show/find the top genes from.

Value

List containing two slots. First is named "plot" and shows a barplot with the top genes and their corresponding loadings. Second is named "genes" and is a dataframe of the genes with highest (in absolute value) loading in the specified low-dimensional directions. There are three columns: gene name, loading value, and which direction it is in. The number of columns is the product of parameters highest and dirs.

Examples

data(MouseData)

wsir_obj = wSIR(X = sample1_exprs,
  coords = sample1_coords,
  optim_params = FALSE,
  alpha = 4,
  slices = 6) # create wsir object
top_genes_obj = findTopGenes(WSIR = wsir_obj, highest = 8)
top_genes_plot = top_genes_obj$plot # select plot
top_genes_plot # print plot