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

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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

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# 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")