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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

flowhelperrr

The goal of flowhelperrr is to help you (me) do flow cytometry analysis in R using data frames.

The main reason this package exists was that I kept re-writting many functions in many of the analyses I did of my flow cytometry data. Therefore, this package is not mean to become available through cran or particularly light on dependencies/imports.

Installation

devtools::install_github("jspaezp/flowhelperrr")

Examples

library(flowhelperrr)
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)

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)

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.