In uhlitz/incucyter: Analysing IncuCyte ZOOM® data in R

incucyter is an R package to read, annotate, normalise and plot IncuCyte ZOOM® metrics.

Installation

if(!library(devtools, logical.return = T)) install.packages("devtools")
if(!library(tidyverse, logical.return = T)) install.packages("tidyverse")
devtools::install_github("uhlitz/incucyter")

Quick start

You can use incucyter to...

1. read + annotate
2. normalise
3. plot

...IncuCyte ZOOM® metrics.

To do so, export your incucyte metrics with IncuCyte ZOOM® software using the following settings. File names are not relevant, all other settings are mandatory for incucyter to properly import the data:

1 read + annotate

Example code to read and annotate incucyte metrics:

library(tidyverse)
library(incucyter)

example_data <- system.file("extdata", 
                            c("sample_data_GO_Confluence_percent.txt",
                              "sample_data_PO_Confluence_percent.txt"),
                            package = "incucyter")

example_annotation <- system.file("extdata", 
                                  "sample_data_annotation.tsv",
                                  package = "incucyter")

incu_tbl <- read_incu(file = example_data,
                      annotation = example_annotation)

Your annotation table must contain four columns: Analysis_Job, Well, Treatment and Reference. You can freely add other columns and use these columns to summarise your data for plotting or summary statistics.

To annotate your table, you can use read_incu with a file path to a tab delimited annotation file or with a R data.frame.

An example annotation can look like this:

library(knitr)
read_tsv(example_annotation) %>% 
  slice(1:20) %>% 
  kable

2 normalise

You can normalise your data to a reference metric and/or to a set of referece wells. For the first, calc_incu_ratios calculates all ratios between the different metrics in your table. These ratios can be plotted with plot_metric like any other metric. For the latter, norm_incu normalises your metrics to a given reference time point and a given set of reference wells (specified as a column in your annotation table, see above).

incu_tbl_comp <- calc_incu_ratios(incu_tbl)
incu_tbl_comp_norm <- norm_incu(incu_tbl_comp, ref_time = 72)

3 plot

You can plot multiple metrics with plot_metrics or a microplate overview plot with plot_microplate.

incu_tbl_comp_norm %>% 
  filter(is.na(siRNA)) %>% 
  plot_metrics(color = c("Treatment", "Inhibition"), 
               label = c("Treatment", "Inhibition"), summarise = T)

incu_tbl %>% 
  filter(Metric == "Green_Confluence") %>% 
  plot_microplate(color = c("Treatment", "Inhibition"))

uhlitz/incucyter documentation built on May 3, 2019, 2:23 p.m.