README.md

In jspaezp/flowhelperrr: Helps you analyze flow cytometry data using data frames

flowhelperrr

The goal of flowhelperrr is to help you do flow cytometry analysis on R using data frames

Installation

devtools::install_github("jspaezp/flowhelperrr")

Examples

library(flowhelperrr)
#> Loading required package: shiny
#> Loading required package: miniUI
library(ggplot2)
## basic example code

Operations using Polygons

Gates can be defined as polygons in a data frame. Such data frames can be used to check what points are inside such polygons.

poly_selection <- data.frame(
    Petal.Length = c(2,4,6),
    Sepal.Width = c(2,4,2))

is_point_in_path(
    iris$Petal.Length,
    iris$Sepal.Width,
    poly_selection)
#>   [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [49] FALSE FALSE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE
#>  [61]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE
#>  [73]  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [85]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [97]  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE
#> [109] FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE
#> [121] FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE
#> [133] FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE
#> [145] FALSE FALSE  TRUE FALSE FALSE FALSE

Since it is vectorized it can be used as well in NSE

iris2 <- dplyr::mutate(
    iris,
    point_in_poly = is_point_in_path(
        Petal.Length,
        Sepal.Width,
        poly_selection))

head(iris2)
#>   Sepal.Length Sepal.Width Petal.Length Petal.Width Species point_in_poly
#> 1          5.1         3.5          1.4         0.2  setosa         FALSE
#> 2          4.9         3.0          1.4         0.2  setosa         FALSE
#> 3          4.7         3.2          1.3         0.2  setosa         FALSE
#> 4          4.6         3.1          1.5         0.2  setosa         FALSE
#> 5          5.0         3.6          1.4         0.2  setosa         FALSE
#> 6          5.4         3.9          1.7         0.4  setosa         FALSE

ggplot(iris, aes(x = Petal.Length, y = Sepal.Width,
                 colour = is_point_in_path(Petal.Length, Sepal.Width, poly_selection))) +
    geom_point() +
    geom_polygon(colour = "gray", alpha = 0.3, data = poly_selection) +
    theme(legend.position = "bottom")

Shiny Gadgets

Gadgets are provided to help with the things that are hard to do exclusively on the command line (such as making an octagonal gate …)

ggpolygon

This gadget allows you to click to form a polygon and returns a data frame that defines such polygon

ggpolygon(iris, "Sepal.Length", "Petal.Length")

To generate the data.frame, type 
'data.frame(c(5.29656915230736, 5.62182752573929, 6.26495203684332, 7.28508057169799, 6.64195606059396), c(4.65156384997072, 3.41011046538746, 3.74383449350124, 4.9852878780845, 6.50706944628333))'
  Sepal.Length Petal.Length
1     5.296569     4.651564
2     5.621828     3.410110
3     6.264952     3.743834
4     7.285081     4.985288
5     6.641956     6.507069

Things to run before commiting

devtools::test()
devtools::build_readme()
devtools::document()
devtools::build_site()

jspaezp/flowhelperrr documentation built on Jan. 1, 2021, 7:10 a.m.