plot_bubble: Bubble plot.

View source: R/PLOT-plot_bubble.R

plot_bubbleR Documentation

Bubble plot.

Description

Creates a bubble plot of the data of bins metabolism

Usage

plot_bubble(tibble_ko, x_axis, y_axis, analysis=c("KEGG","INTERPRO", "DBCAN"),
data_experiment=NULL, calc=NULL, color_character=NULL, order_bins=NULL, 
order_metabolism=NULL, color_pallet=NULL, range_size=NULL, x_labs=TRUE,
y_labs=TRUE, text_x=NULL, text_y=NULL)

Arguments

tibble_ko

a tibble object, created with the read_* mapping_ko and get_subset_* functions.

x_axis

a string, a column name of the metabolism table. It determined the x axis label.

y_axis

a string, a column name of the metabolism table. It determined the y axis label.

analysis

a character indicating if your input data are from KEGG, INTERPRO or DBCAN

data_experiment

optional. a data frame object containing metadata information.

calc

a character indicating with type of calc should be done to plot the results. Valid values are "Abundance", "Binary", "Percentage", and "None". If you chose none you are expected to use a tibble table obtained from calc_binary or calc_percentage.

color_character

optional. a string column name of the metadata or metabolism object, used for color.

order_bins

optional. a character vector indicating the bin order.

order_metabolism

optional. a character vector indicating metabolism order.

color_pallet

optional. a character vector of colors to use.

range_size

optional. a numeric vector indicating the range size of the dots.

x_labs

optional. If FALSE it will set the x lab to NULL.

y_labs

optional. If FALSE it will set the y lab to NULL.

text_x

optional. A numeric vector indicating the size of the x text letters.

text_y

optional. A numeric vector indicating the size of the y text letters.

Details

This function is part of a package used for the analysis of bins metabolism.

Examples

plot_bubble(tibble_ko=ko_bin_mapp, x_axis=Bin_name, y_axis=Module, 
analysis="KEGG", data_experiment=metadata, calc="Binary",
color_character=Clades)

mirnavazquez/RbiMs documentation built on Nov. 20, 2024, 1:16 a.m.