GOBubble {GOplot}

Bubble plot.

Description

The function creates a bubble plot of the input data. The input data can be created with the help of the circle_dat function.

Usage

GOBubble(data, display, title, colour, labels, ID = T, table.legend = T,
  table.col = T, bg.col = F)

Arguments

data

A data frame with coloumns for category, GO ID, term, adjusted p-value, z-score, count(num of genes)

display

A character vector. Indicates whether it should be a single plot ('single') or a facet plot with panels for each category (default='single')

title

The title (on top) of the plot

colour

A character vector which defines the colour of the bubbles for each category

labels

Sets a threshold for the displayed labels. The threshold refers to the -log(adjusted p-value) (default=5)

ID

If TRUE then labels are IDs else terms

table.legend

Defines whether a table of GO ID and GO term should be displayed on the right side of the plot or not (default = TRUE)

table.col

If TRUE then the table entries are coloured according to their category, if FALSE then entries are black

bg.col

Should only be used in case of a facet plot. If TRUE then the panel backgrounds are coloured according to the displayed category

Details

The x- axis of the plot represents the z-score. The negative logarithm of the adjusted p-value (corresponding to the significance of the term) is displayed on the y-axis. The area of the plotted circles is proportional to the number of genes assigned to the term. Each circle is coloured according to its category and labeled alternatively with the ID or term name.If static is set to FALSE the mouse hover effect will be enabled.

Examples

## Not run: 
#Load the included dataset
data(EC)

#Building the circ object
circ <- circular_dat(EC$david, EC$genelist)

#Creating the bubble plot colouring the table entries according to the category
GOBubble(circ, table.col = T)

#Creating the bubble plot displaying the term instead of the ID and without the table
GOBubble(circ, ID = F, table.legend = F)

#Faceting the plot
GOBubble(circ, display = 'multiple')

## End(Not run)