Inspect samples detected having more than 1 nucleus

Load data

Load image QC table - for now it has only number of nuclei detected in each sample now. This table does not include all of the single cell samples, and the ones that are not included are the samples classifed as no DNA content in DAPI images.

The summary table contains three columns:

plate: labeled by the mix of individual cell lines
well: labels assigned by the JULI imaging system. These will be converted to correspond to C1 plate labels (rows and columns).
nnuclei: number of nuclei detected in a single cell sample

nuclei_table <- readRDS("/project2/gilad/joycehsiao/fucci-seq/output/image-qc.rds")

with(nuclei_table, table(nnuclei))

nnuclei
   0    1    2    3    4    5    6    7    8   12   20 
   4 1029  112   44   15   13    1    2    2    1    1 

Inspect samples with 12 nuclei.

nuclei_table[which(nuclei_table$nnuclei == 12),]

        nnuclei  well       plate
0004812      12 00048 19160_18870

Inspect samples with 20 nuclei.

nuclei_table[which(nuclei_table$nnuclei == 20),]

       nnuclei  well       plate
000636      20 00063 18870_19160

Printing images for inspection

This section is for record keeping. All images for samples with more than 1 nucleus detected have been converted to PNG format and stored in /project2/gilad/fucci-seq/images_inspect.

First select samples for inspection. The code below selects from plate 18511_18855 the samples that have two nuclei detected.

cases <- nuclei_table[which(nuclei_table$nnuclei == 2 & nuclei_table$plate == "18511_18855"),]

Extract the wells labels and convert to a character variable.

wells <- as.character(cases$well)

wells <- c("00012","00032","00044","00047","00051","00052","00067","00076","00085","00088","00096")

print(wells)

 [1] "00012" "00032" "00044" "00047" "00051" "00052" "00067" "00076"
 [9] "00085" "00088" "00096"

The code below will save images in png format at /project2/gilad/fucci-seq/images_inspect.

#' @param wells vector of wells ID (use the format specified above).
#' @param plate plate ID

print_png <- function(plate, wells) {
  for (index in 1:length(wells)) {
    id <- wells[index]
    dir_images_data_pl <- paste0("/project2/gilad/fucci-seq/images_curated/",plate,"/")
    dir_output <- "/project2/gilad/fucci-seq/images_inspect/"
    bright <- readImage(paste0(dir_images_data_pl, "BRIGHT/", id, ".TIFF"))
    dapi <- readImage(paste0(dir_images_data_pl, "DAPI/", id, ".TIFF"))
    gfp <- readImage(paste0(dir_images_data_pl, "GFP/", id, ".TIFF"))
    rfp <- readImage(paste0(dir_images_data_pl, "RFP/", id, ".TIFF"))
    
    writeImage(bright, paste0(dir_output, plate,".",id,".bright.png"))
    writeImage(dapi, paste0(dir_output, plate,".",id,".dapi.png"))
    writeImage(gfp, paste0(dir_output, plate,".",id,".gfp.png"))
    writeImage(rfp, paste0(dir_output, plate,".",id,".rfp.png"))
    # combo <- combine(dapi, bright, gfp, rfp)
    # writeImage(combo, paste0(dir_output, plate,".",id,".combo.png"))
  }
}


plates <- c("18511_18855","18855_19101","18855_19160","18870_18511",
            "18870_18855","18870_19101","18870_19160","19098_18511",
            "19098_18870","19098_19160","19101_18511","19101_19098",
            "19160_18870","18855_19098","19101_19160","19160_18511")

for (index in 1:length(plates)) {
  plate <- plates[index]
  cases <- nuclei_table[which(nuclei_table$nnuclei > 1 & nuclei_table$plate == plate),]
  wells <- as.character(cases$well)
  print_png(plate, wells) 
}

Session information

sessionInfo()

R version 3.4.1 (2017-06-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Scientific Linux 7.2 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_3.4.1  backports_1.1.1 magrittr_1.5    rprojroot_1.2  
 [5] tools_3.4.1     htmltools_0.3.6 yaml_2.1.14     Rcpp_0.12.13   
 [9] stringi_1.1.5   rmarkdown_1.6   knitr_1.17      git2r_0.19.0   
[13] stringr_1.2.0   digest_0.6.12   evaluate_0.10.1