README.Rmd

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# toccatr 



***********************



A Toccata is a musical piece with fre-flowing harmonies. **toccatr** is a collection of tools for importing data from [Harmony]("https://www.revvity.com/gb-en/product/harmony-5-2-office-revvity-hh17000019") 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.


## <i class="fa fa-cog" aria-hidden="true"></i> Installation

toccatr is not on CRAN. To install the latest version use:


```r
install.packages("devtools")
library(devtools)
```



## Using 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  
* `u()` List unique items in a variable in df dataframe  
* `loggy()` Log transform all numeric variables  

**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.