normentR

The very much unofficial package with tools to create plots in ggplot using the NORMENT house style and other functionality tools useful for R users at NORMENT. Some example uses of this package are discussed here.

Installation

This package is not available on CRAN, and likely won't be for the forseeable future. The only way to install it is by either getting the source file for installation on the TSD or any other machine without internet connection or installing it using the {devtools} package (which is recommended). The latter option requires the {devtools} package to be installed. Alternatively, it's possible to install the source package by downloading this package from the GitHub, by downloading a source file from the wiki, or by asking Daniel for the source file.

# On TSD
install.packages("/cluster/projects/p33/users/dtroelfs/software/R/normentR_0.1.4.tar.gz", type = "source", repos = NULL)

# Anywhere else
devtools::install_github("norment/normentR")

Functionality

The functions and tools in this package are, plotting, statistics, and functionality: For plotting:

theme_norment()
scale_color_norment()
scale_fill_norment()
available_palettes()
show_norment_palette()
show_norment_logo()
shift_axes()

For statistics:

FWER()
cohens_d()
get_outliers()
sem()
signed_rank()
sine()

And for functionality:

clear()
get_upper_half_matrix()
get_lower_half_matrix()
get_full_matrix()
%!in%
simulate_corr_matrix()
simulateGWAS()

There are a few other scripts in this package, which are mainly used for color definitions and scripts to create the color definitions into formats that can be used with the ggplot() function. More functionality will be added over time.

Statistics

This package contains functions to extract some statistical properties from data, such as the effect size (cohens_d()), the standard error of the mean (sem()) and the family-wise error rate (FWER()).

Functionality

The %in% operator is very useful, but sometimes one would like to extract the values that do NOT exist in another data frame. It is possible to just wrap the %in% operator in a negation, but I felt it was more intuitive to create a function that states more explicitely what it's doing, the %!in% function. This function particularly useful in cases where you need to find participants that do not exist in one datafile, so you can track the data from these individuals down down. Over the duration of a long coding session in R, the workspace with the variables can clog up somewhat. The clear() function attempts to answer some of this. It is nothing more than a wrapper for the rm function, but it takes simpler input. It's possible to either remove all variables (clear()), remove specific variables only (either individuals or matching a string (clear("data_*"))), or remove all variables except an individual variable or variables matching a string (clear(keep = "data")).

Simulate GWAS data

The simulateGWAS() function generates a simulated dataset with similar properties to the PLINK output of the --assoc flag. Columns, values, and properties are similar to a regular GWAS from a UK Biobank sample with a quantitative phenotype.

Color Palettes

All colors used in this package come from either the NORMENT design guide, or colors frequently used by NORMENT (such as in the logo or the order of the colors as used in the Powerpoint templates). Possible options for the color palette are stored in the function available_palettes(). To view all color palattes, type: show_norment_palette(). To view only one or more palettes, submit them as arguments into the last function as such: show_norment_palette(c("default","gradient")). In addition to the NORMENT colors, I also added color schemes from the scico package, which contains a bunch of scientific color palettes for various purposes. These color palettes were developed by Fabio Crameri, researcher at the Centre for Earth Evolution and Dynamics, also at the University of Oslo. A paper on these color palettes has been published (also see here). The color palettes in the scico package are in most cases superior to the standard color palettes provided by ggplot2 (and the NORMENT color palettes) and can be interpreted by for individuals with color-blindness too.

Extensions that cannot be added to the ggplot object directly

There are two functions that cannot be added as an element to a ggplot object, but (for now) only work as a function that takes the the ggplot object as input. There can be used like shown below:

# Add NORMENT logo to plot
show_norment_logo(plot.obj)

# Shift axes to specific place on x- and y-axes
shift_axes(plot.obj, x = 0, y = 0)