plot_single_gene {EMMIXgene} | R Documentation |
Plot a single gene expression histogram with best fitted mixture of t-distributions according to the EMMIX-gene algorithm.
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
)
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. |
A ggplot2 histogram with fitted t-distributions overlayed.
example <- plot_single_gene(alon_data,1)
#plot(example)