dotPercentage {eegc} | R Documentation

## Percentage Calculation and Visualization

### Description

This function calculate the percentage of genes in each category over given annotated gene sets and plot the percentages.

### Usage

    dotPercentage(cate.gene, annotated.gene, order.by = NULL, type = "l", lty = 1,
    pch = NULL, col = NULL, srt = 50, font = 1, adj = c(1,1), cex = 1, add.line = TRUE,
    legend = TRUE, legend.label = NULL, ...)

### Arguments

`cate.gene` | a list of the five gene categories, alternatively output by `categorizeGene`.
`annotated.gene` | a list of the annotated gene sets which the `cate.gene` are proportioned in.
`order.by` | one character out of of "Reversed","Inactive","Insufficient","Successful" and "Over" to specify a gene category the percentage is ordered by.
`type, lty, pch, col` | parameters for the plotting, specifying the type of plotting; the line type when `type` is "l"; the symbol of points on the line; and the color of lines, see graphic parameters in `par`().
`srt, font, cex, adj` | parameters for the text labeled on x-axis, specifying the string rotation in degrees; the font of text; the text size, see graphic parameters in `par`().
`add.line` | logical to determine if to add lines on the dots, logical to `TRUE`.
`legend` | logical to determine whether the legend is added on the figure, default to `TRUE`.
`legend.label` | labels of the legend, applied only when `legend` is `TRUE`.
`...` | other parameters see `plot`.

### Value

a data frame with the percentage of `cate.gene` in the `annotated.gene`.

### Examples

    # load the C/T-specific genes in 16 cells/tissues
    data(human.gene)
    data(cate.gene)
    # perc = dotPercentage(cate.gene = cate.gene, annotated.gene = human.gene,
    #                     order.by = "Successful")

[Package eegc version 1.12.0 Index]