###Example workflow 1: open a file -> plot using createplotlist - save the plots
###Renske v Raaphorst - October 2019

################Packages################

require(bactMAP)

################Variables - automatic###

# This workflow imports data from oufti and assumes both segmentation as spot detection data.

# Check all import functions on https://github.com/veeninglab/bactmap/wiki/importing-data-using-bactmap

# Set your working directory using 'choose.dir'

setwd(choose.dir())

# Pick your Oufti output file using `file.choose()`

oufti_file_location <- file.choose()

# Give the proper conversion factor for "My_Factor". 
# The console will ask for the factor when running the script.

addPixels2um("My_Factor")


###########Data_Import#####################
###########################################


oufti_output <- extr_Oufti(oufti_file_location)


##########Plotting#########################

#No side plots, 4 groups (default), blue colors.

oufti_plots <- createPlotList(oufti_output$spots_relative, 
                              oufti_output$mesh,
                              mag="My_Factor",
                              colorpalette="ColdBlue",
                              showPlot=FALSE)

############Saving Data###################

#save relative spot localizations
save(oufti_plots$spotdata, file="Oufti_Spots_Relative.Rda")

#save all plots

cairo_pdf(filename="All_Oufti_Plots.pdf", onefile=TRUE, width=8, height=8)

oufti_plots$lengthplot

oufti_plots$widthplot

plot(oufti_plots$qplots)

oufti_plots$plottotal

plot(oufti_plots$histograms)

dev.off()