vignettes/easyXpress.R

In AndersenLab/easyXpress: A Package to Read, Process, and Analyze Worm Data Generated from CellProfiler’s WormToolbox

## ---- include = FALSE---------------------------------------------------------------------------------------------------------------------------
knitr::opts_chunk$set(
  fig.align = "center",
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------------------------------------------------------------------------
library(easyXpress)

## ----message=FALSE------------------------------------------------------------------------------------------------------------------------------
## In this example, there is no design file. As such, the argument design = FALSE

# Define experimental directory and file name
dirs <- rprojroot::find_package_root_file("vignettes", "example_data")
datafile <- "CellProfiler-Analysis_20191119_example_data.RData"

# Read in the data
raw <- easyXpress::readXpress(filedir = dirs, rdafile = datafile, design = FALSE)

## ----echo=FALSE, message=FALSE, warning=FALSE---------------------------------------------------------------------------------------------------
library(tidyverse)
subset <- raw %>%
  dplyr::filter(model == "L1") %>%
  dplyr::select(Metadata_Experiment,Metadata_Plate,Metadata_Well,Image_FileName_RawBF,model, worm_length_um) 
knitr::kable(subset[1:4,], caption = "Subset of data frame")

## ----message=FALSE------------------------------------------------------------------------------------------------------------------------------
model_selected <- easyXpress::modelSelection(raw)

## ----echo=FALSE---------------------------------------------------------------------------------------------------------------------------------
subset <- model_selected
knitr::kable(subset[1:4,1:9], caption = "Subset of data frame")

## -----------------------------------------------------------------------------------------------------------------------------------------------
edge_flagged <- easyXpress::edgeFlag(model_selected, radius=825, center_x=1024, center_y=1024)

## ----message=FALSE------------------------------------------------------------------------------------------------------------------------------
raw_flagged <- easyXpress::setFlags(edge_flagged, cluster_flag = TRUE, well_edge_flag = TRUE)

## ----message=FALSE, paged.print=TRUE------------------------------------------------------------------------------------------------------------
processed <- easyXpress::process(raw_flagged, Metadata_Plate, Metadata_Well)

## ----echo=FALSE---------------------------------------------------------------------------------------------------------------------------------
knitr::kable(summary(processed), caption = "Processed list items")

## ----message=FALSE------------------------------------------------------------------------------------------------------------------------------
processed <- easyXpress::Xpress(filedir = dirs, rdafile = datafile, Metadata_Plate, Metadata_Well)

## ----include=FALSE------------------------------------------------------------------------------------------------------------------------------
rfile <- rprojroot::find_package_root_file("vignettes", "example_data", "cp_data", "processed_plate_data.RData")
load(rfile)


## ----fig.height=5, fig.width=8------------------------------------------------------------------------------------------------------------------
## This example uses a new dataset. Reading & processing of this dataset is not shown ##

# To start, save summarized_processed list element to new variable:
# processed_plate_data <- processed[[4]]

# view plate
easyXpress::viewPlate(processed_plate_data, "p61")


## ----fig.height=5, fig.width=7------------------------------------------------------------------------------------------------------------------
## This example shows the processed data

# Saving processed_data list element to new variable
proc_data <- processed[[2]]

# Define processed image directory
proc_img_dir <- rprojroot::find_package_root_file("vignettes", "example_data", "ProcessedImages")

easyXpress::viewWell(proc_data, proc_img_dir, "p61", "C02", boxplot = TRUE) 

## ----include=FALSE------------------------------------------------------------------------------------------------------------------------------
rfile <- rprojroot::find_package_root_file("vignettes", "example_data", "cp_data", "processed_dose_data.RData")
load(rfile)

## ----fig.height=4, fig.width=10-----------------------------------------------------------------------------------------------------------------
## This example uses a new dataset. Reading & processing of this dataset is not shown ##

# Saving data elements to new variable
proc_dose_data <- processed_dose_data[[2]]
raw_dose_data <- processed_dose_data[[1]]

# Define processed image directory
proc_img_dir <- rprojroot::find_package_root_file("vignettes", "example_data", "ProcessedImages")

# View example images and object types from raw or processed dose response data
plot_proc <- easyXpress::viewDose(proc_dose_data, strain_name = "PD1074", drug_name = "paraquat", proc_img_dir = proc_img_dir) 
plot_raw <- easyXpress::viewDose(raw_dose_data, strain_name = "PD1074", drug_name = "paraquat", proc_img_dir = proc_img_dir) 

## showing processed dose response data only ##
plot_proc