r-lolliplots

This is the lolliplots tool, converted to be able to be run in R.

A tool to create lollipop plots (lolliplots) for coding region association results

Setup

The plotly package will need to be installed to run this script. To install plotly, use the command install.packages("plotly")

Loading it into your own script

Lolliplots is not currently a CRAN-available package, and so needs to be imported by sourcing the lolliplots.R file to your current system. This can be done with the following:

source("lolliplots.R")

An absolute file path to lolliplots.R may need to be given to source the file correctly.

You should then be able to use the functions as normal.

Exon location data will need to be downloaded only once. This can be run using get_exon_data()

This will open a prompt to download the biomart data.

read_exon_locs() should be given the file that was downloaded using get_exon_data().

This data should then be filtered to the desired transcript before plotting: exons[which(exons[, 'Transcript.stable.ID'] == transcript_id),] Where transcript_id is the name of your desired transcript

Use reduced_gap <- reduce_gaps(assoc, selected_exons_df) to remove introns from the association data and exon location data before passing the new data to lolliplot_raw(). Data should be accessed from the reduce_gaps() output using reduced_gap$results and reduced_gap$exons

Functions

get_exon_data():

Arguments: None

Run this command (No need to put into a variable) to download the exon location data. Downloads the data to a new folder in the current working directory: ensembl_exon_positions/b38_downloaded This only need to be run once. In subsequent runs, this should be loaded in using read_exon_locs() through your own hard coded location. User inputs will be requested.

read_exon_locs(file):

Arguments	About
file	string: the file location of the downloaded exon data (eg "ensembl_exon_positions/b38_downloaded")

Function reads in the downloaded file data using pandas and assigns the appropriate headers to work with the default options of lolliplot_raw() Column names are as follows:

• Gene.stable.ID
• Transcript.stable.ID
• Exon.start_bp
• Exon.stop_bp
• Gene.start_bp
• Gene.end_bp
• Gene.name
• Exon.Name

reduce_gaps(gene_results, exon_info)

Arguments	About	Default
gene_results	data.frame: A dataframe of the association results to plot	-
exon_info	data.frame: A dataframe of the filtered exon locations	-
new_gap	numeric: New gap size between the exons	10
ex_start_col	string: Name of column of exon_info of exome start locations	'Exon.start_bp'
ex_stop_col	string: Name of column of exon_info of exome stop locations	'Exon.stop_bp'
gene_pos_col	string: Name of column of gene_results of the variant positions	'GENPOS'

Reduce the spaces between the coding regions to a smaller gap (designated by new_gap). Returns one lsit with two named attributes, results and exons, the modified gene_results and the modified exon_info respectively. The resulting dataframes can be used to make the lolliplots with the intronic regions removed.

Note: the exon_info should be filtered to your desired transcript before inputting into reduce_gaps() or lolliplot_raw().

lolliplot_raw(results, exon_info, title)

Arguments	About	Default
results	data.frame: : A dataframe of the association results to plot, or the results output of reduce_gaps()	-
exon_info	data.frame: : A pandas dataframe of the filtered exon locations, or the exons output of reduce_gaps()	-
title	string: Title of the plot	-
fig_height	int: Figure height (can be adjusted using update_layout())	500
fig_width	int: Figure height (can be adjusted using update_layout())	1400
ex_start_col	string: Name of column of exon_info of exome start locations	'Exon.start_bp'
ex_stop_col	string: Name of column of exon_info of exome stop locations	'Exon.stop_bp'
lolli_x	string: Name of column of results df for x axis	'GENPOS'
lolli_y	string: Name of column of results df for y axis	'LOG10P'
lolli_size	string: Name of column of results df for size of bubbles	'BETA'
lolli_col	string: Name of column of results df for colour of bubbles	'MASK'
lolli_direction	string: Name of column of reults df for direction of bubbles	'BETA'
lollipop_max_size	float: Maximum size of bubbles (Note this need to be a decimal, not an integer)	5.
lollipop_stem_width	float: Width of the lollipop stems	0.1

Returns a lolliplot as a plotly figure.

Note: the exon_info should be filtered to your desired transcript before inputting into reduce_gaps() or lolliplot_raw().

lp.example():

Arguments: None

This is an example lolliplot script, using available associations on the Exeter server. This function can be modified and run to get lolliplots out quickly and easily. To save the figures, the print() parts should be commented out, and the htmlwidgets::saveWidget()should be uncommented. The name of the output file should be changed from lolliplots_example.html.