## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, results = "markup", message = FALSE, warning = FALSE) ## ----------------------------------------------------------------------------- library(Sconify) # Example fcs file basal <- system.file('extdata', 'Bendall_et_al_Cell_Sample_C_basal.fcs', package = "Sconify") # Run this, and check your directory for "markers.csv" markers <- GetMarkerNames(basal) markers ## ----eval = FALSE------------------------------------------------------------- # # Turn this into two columns, one for surface markers, and one for phosphos # # Label the two columns accoridngly. Save to csv. You'll read this modified # # file in the ProcessMultipleFiles() function. # write.csv(markers, "markers.csv", row.names = FALSE) ## ----out.width = "200px", eval = TRUE----------------------------------------- knitr::include_graphics("original.markers.csv.example.png") ## ----out.width = "200px"------------------------------------------------------ knitr::include_graphics("modified.markers.csv.example.png") ## ----------------------------------------------------------------------------- # FCS file provided in the package basal <- system.file('extdata', 'Bendall_et_al_Cell_Sample_C_basal.fcs', package = "Sconify") # Example of data with no transformation basal.raw <- FcsToTibble(basal, transform = "none") basal.raw # Asinh transformation with a scale argument of 5 basal.asinh <- FcsToTibble(basal, transform = "asinh") basal.asinh ## ----------------------------------------------------------------------------- # The FCS files (THEY NEED TO BE IN THE "....._condidtion.fcs" format") basal <- system.file('extdata', 'Bendall_et_al_Cell_Sample_C_basal.fcs', package = "Sconify") il7 <- system.file('extdata', 'Bendall_et_al_Cell_Sample_C_IL7.fcs', package = "Sconify") # The markers (after they were modified by hand as instructed above) markers <- system.file('extdata', 'markers.csv', package = "Sconify") markers <- ParseMarkers(markers) surface <- markers[[1]] surface ## ----------------------------------------------------------------------------- # Combining these. Note that default is sub-sampling to 10,000 cells. # Here, we subsample to 1000 cells to minimize processing time for the vignettes. # not normalizing, and not scaling. wand.combined <- ProcessMultipleFiles(files = c(basal, il7), input = surface, numcells = 1000) wand.combined unique(wand.combined$condition) # Limit your matrix to surface markers, if just using those downstream wand.combined.input <- wand.combined[,surface] wand.combined.input ## ----------------------------------------------------------------------------- # We can do this on a single file as well. wand.basal <- ProcessMultipleFiles(files = basal, numcells = 1000, scale = TRUE, input = surface) wand.basal unique(wand.basal$condition) ## ----------------------------------------------------------------------------- # Using the aforementioned basal fcs file markers <- system.file('extdata', 'markers.csv', package = "Sconify") # The markers markers <- read.csv(markers, stringsAsFactors = FALSE) surface <- markers$surface # The function split.data <- SplitFile(file = basal, input.markers = surface, numcells = 1000) split.data unique(split.data$condition)