Quantify Genes and Corresponding ED ratios in Each Category

Description

Quantify genes in each gene category and their expression difference (ED) ratios in a density plot.

Usage

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densityPlot(ratio, color = NULL, main = NA, xlab = NA, ylab = "Density",
legend.labels = NULL, shade = TRUE, transparency = TRUE, proportion = TRUE,
out.file = NULL, ...)

Arguments

ratio

a list of ED ratios for five gene categories, alternatively output by categorizeGene.

color

vector of colors for the five gene categories.

main, xlab, ylab

the overall title, tile for x axis, and title for y axis, see title.

legend.labels

vector of labels for the legend.

shade

logical to determine if the five categories are filled with shades.

transparency

logical to determine if the density plot is transparent.

proportion

logical to determine whether the proportion of each category genes over the all genes is drawn on the density plot.

out.file

a character string naming the output file with density plot.

...

parameters in plot.

Value

a density plot

Examples

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data(cate.ratio)
names(cate.ratio)
# make the extreme ED ratios in Reversed and Over categories to the median values
reverse = cate.ratio[[1]]
over = cate.ratio[[5]]
reverse[reverse[,1] <= median(reverse[,1]), 1]  = median(reverse[,1])
over[over[,1] >= median(over[,1]),1] = median(over[,1])
cate.ratio[[1]] = reverse
cate.ratio[[5]] = over

# densityPlot(cate.ratio, xlab = "ED ratio", ylab = "Density", proportion = TRUE)