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

1 2 3 |

`ratio` |
a list of ED ratios for five gene categories, alternatively output by |

`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 |

`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 |

a density plot

1 2 3 4 5 6 7 8 9 10 11 | ```
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)
``` |

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