<!-* README.md is generated from README.Rmd. Please edit that file –>
A Toccata is a musical piece with fre-flowing harmonies. toccatr is a collection of tools for importing data from Harmony high content imaging software, as well as simple data manipulation and visualisation tools
The main toccatr functions:
- import PlateResults.txt files from multiple subfolders;
- make plate layout maps, and heatmaps of data in 96 well format; and
- reshape the data suitable for graphing in Graphpad Prism.
toccatr is not on CRAN. To install the latest version use:
install.packages("devtools")
library(devtools)
install_github("jsmithss/toccatr")A full lit of functions is found below:
Importing and exporting data
* harmread_pl() Read multiple plate results files into one
dataframe
* harmread_ob() Read multiple object results files
* clipfromxl() Copy data from clipboard (Excel) to R
* clip2xl() Copy data from R dataframe to clipboard for pasting to
Excel
* clip2csv() Copy data from R dataframe to csv format
* prismy_col() Reformat data for Prism column tables
Data frame tools
* jiggle() Move all text columns to the left of the dataframe
* coslectr() Interactively select columns - useful for large data
frames
* repspace() Replace underscore with space
* repunderscore() Replace space with underscore
* rescale_z() Z-score a variable
* well2row() Creates numeric row and column references from Well
name
* squish() Limit upper and lower values of variable
* %nin%() Select items Not in a list
Visualisation
* platemap() 96 well plate layouts by compound or treatment
* hotplate() Heatmap of data by plate position
* barchartr() Quick barcharts with mean and SD
* majsty() Interactive Scatter plots, drag to highlight points
* ploxy() Interactive scatter plots with annotation and zoom
* ploxytime() Interactive scatter plots with animation
* theme_js() James ggplot theme
* theme_tt() Clean ggplot theme
* theme_ttf() Clean ggplot theme for faceted data
* tubemap() List of colours based on London Tube map
Toccatr is very much a work in progress, suggestions and contributions welcome.