plot_single_gene {EMMIXgene}

Plot a single gene expression histogram with best fitted mixture of t-distributions.

Description

Plot a single gene expression histogram with best fitted mixture of t-distributions according to the EMMIX-gene algorithm.

Usage

plot_single_gene(
  dat,
  gene_id,
  g = NULL,
  random_starts = 8,
  max_it = 100,
  ll_thresh = 8,
  min_clust_size = 8,
  tol = 1e-04,
  start_method = "both",
  three = TRUE,
  min = -4,
  max = 2
)

Arguments

dat

matrix of gene expression data.

gene_id

row number of gene to be plotted.

g

force number of components, default = NULL

random_starts

The number of random initializations used per gene when fitting mixtures of t-distributions. Initialization uses k-means by default.

max_it

The maximum number of iterations per mixture fit. Default value is 100.

ll_thresh

The difference in -2 log lambda used as a threshold for selecting between g=1 and g=2 for each gene. Default value is 8, which was chosen arbitrarily in the original paper.

min_clust_size

The minimum number of observations per cluster used when fitting mixtures of t-distributions for each gene. Default value is 8.

tol

Tolerance value used for detecting convergence of EMMIX fits.

start_method

Default value is "both". Can also choose "random" for purely random starts.

three

Also test g=2 vs g=3 where appropriate. Defaults to TRUE.

min, max

Minimum and maximum x-axis values for the plot window.

Value

A ggplot2 histogram with fitted t-distributions overlayed.

Examples

example <- plot_single_gene(alon_data,1) 
#plot(example)