[FIXED] How do i use R to input a number of grouping values and recieve an output of observations in a 8x6 grid?

Issue

I'm a newbie to the world of coding/programming. Loving the challenge so far but I've hit a bit of a roadblock.

I'm attempting to automate genotyping preparation for my job as a lab technician.

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Unnecessary background:

I take care of a colony of 500-600 mice with 40-50 given genotype constructs at any given time. Whenever I get new litters (depending on the genotype of the parents) I have to extract DNA and confirm the genotype of the offspring. The task and the challenge of trouble-shooting the process were fun at first but it's getting very mundane and repetitive now. So I've started using R to automate certain parts of my job.

TL/DR: My job is getting repetitive, I want R to help out with that.

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So, in essence, I have an archive of mice as follows. I grouped them by the temperature requirements for the genotyping process and by the number of times I need to genotype the DNA samples.

Mouse ID  Genotype   Gender  Age       Litter_ID   PCR_Temp  Rxns
ZDP658    zDC.Cre       F    4.9        B23844-1      Z        1
ZDP659    zDC.Cre       F    4.9        B23844-1      Z        1
ZDP631    Villin.Cre    F    4.9        B23745-2      Y        1
ZDP575    K14.CreER     M    5.3        B23744-2      Z        1
ZDO931    K14.CreER     M    8.6        B23744-1      Z        1
ZDO932    K14.CreER     M    8.6        B23744-1      Z        1
ZDO933    K14.CreER     M    8.6        B23744-1      Z        1
ZDQ31     Rosa.TSLP     M    3.4        B23701-2      Z        2
ZDQ32     Rosa.TSLP     M    3.4        B23701-2      Z        2

My goal is to receive an output of the individual Mouse_ID's in an 8x6 grid grouped by their "PCR_Temps" and multiplied by their "Rxns" in a zigzag order if possible with two extra spaces per genotype group.

My vision of the output is as follows. I would want to input the Litter_ID of the litters that need genotyping and receive the following.

The honeycomb structure is not necessary. A simple rectangular grid works perfectly fine. The same goes for the zigzag format. Both of those aspects of the output format would be nice but aren't a requirement.

Every group of genotypes would need one space for positive control samples and one space for Wild type/Neg control samples. The genotypes that have a value of "2" or more would be repeated as many times as their "Rxns" value states.

I'm sorry if this question is too dense to follow or code for. I have so far been working with dplyr and ggplot to manipulate and visualize my mouse archives but this particular problem has me at a loss.

If anyone could even point me in the direction of a package that could get me started I would really appreciate it.

So far I have tried some combinations of dplyr and purrr with no success. I have thought of ways to use for loops but have come up empty.

Thank you in advance for any advice.

Solution

Here's an approach with the help of dplyr, grid and gridExtra.

Please excuse the hot mess that is my variable naming convention.

Your data was not complex enough to make a good system, so I generated some random data. Find that at the very end.

First, lets define our litters and filter the mouse data.

library(dplyr)
library(grid)
library(gridExtra)

geno.litters <- c("B23701-2", "B23744-1", "B23844-1","B23944-1")
mice <- data %>% 
            filter(Litter_ID %in% geno.litters) %>%
            arrange(Litter_ID,MouseID) %>%
            split(.,.$PCR_Temp)

mice is now a list of the mice split into plates by PCR temperature.

Let's define a custom function to add positive and negative controls and duplicate rows for those genotypes that need duplicates. We can apply that function to every list element with lapply.

addControlSlots <- function(x){
  genotypes <- unique(x$Genotype)
  genotype.dfs <- list()
  for ( i in seq_along(genotypes)){
    litter.mice <- x[x$Genotype == genotypes[i],]
    litter <- litter.mice[1,"Litter_ID"]
    Temp <- litter.mice[1,"PCR_Temp"]
    litter.mice <- rbind(litter.mice,litter.mice[litter.mice$Rxns == 2,])
    litter.mice <- litter.mice[order(litter.mice$MouseID),]
    control.rows <- data.frame(Litter_ID = litter, MouseID = c("PosCont","NegCont"),Gender = NA,Genotype = genotypes[i], PCR_Temp = Temp, Rxns = 1)
    genotype.dfs[[i]] <- rbind(litter.mice,control.rows)
  }
do.call(rbind,genotype.dfs)
}

processed.temps <- lapply(mice,addControlSlots)
processed.temps[[2]]
#$Z
#    Litter_ID MouseID Gender  Genotype PCR_Temp Rxns
#1    B23701-2   ZO960      F   zDC.Cre        Z    1
#2    B23701-2   ZP810      F   zDC.Cre        Z    1
#3    B23701-2   ZP992      M   zDC.Cre        Z    1
#4    B23701-2 PosCont   <NA>   zDC.Cre        Z    1
#5    B23701-2 NegCont   <NA>   zDC.Cre        Z    1
#...15 more rows

We now have controls after every genotype.

Now let's define a function to fill in the PCR plate. And again apply it to the list.

makePCRPlate <- function(x){
  mouse.vector <- as.character(x$MouseID)
  plate.vector <- rep(NA,6*8)
  plate.vector[1:length(mouse.vector)] <- mouse.vector
  wide <- matrix(plate.vector,nrow=2,byrow = FALSE)
  rbind(wide[,1:8],wide[,9:16],wide[,17:24])
} 

pcr.plates <- lapply(processed.temps,makePCRPlate)
pcr.plates[[2]]
#     [,1]      [,2]      [,3]      [,4]    [,5]    [,6]    [,7]    [,8]   
#[1,] "ZO960"   "ZP992"   "NegCont" "ZO214" "ZP333" "ZP455" "ZP478" "ZQ130"
#[2,] "ZP810"   "PosCont" "ZO214"   "ZP333" "ZP455" "ZP478" "ZQ130" "ZQ875"
#[3,] "ZQ875"   "NegCont" NA        NA      NA      NA      NA      NA     
#[4,] "PosCont" NA        NA        NA      NA      NA      NA      NA     
#[5,] NA        NA        NA        NA      NA      NA      NA      NA     
#[6,] NA        NA        NA        NA      NA      NA      NA      NA    

We can see that the samples have been filled in in the zig-zag pattern.

Now let's use grid to make a .pdf file with the layouts.

pdf("MyPCRPlates.pdf")
for(i in seq_along(pcr.plates)){
  grid.newpage()
  grid.table(pcr.plates[[i]])
  grid.text(paste0("PCR Temp ",names(pcr.plates)[i]),y = unit(0.9,"npc"))
}
dev.off()  

The .pdf file should have a page for each temperature.

Data

set.seed(1)
data1 <- data.frame("MouseID" = paste0("Z",sample(c("O","P","Q"),size = 50,replace = TRUE),round(runif(50,1,999))),
Litter_ID = sample(c("B23701-2", "B23744-1", "B23744-2", "B23745-2", "B23844-1","B23944-1", "B23944-2", "B23951-1"),size=50, replace = TRUE),
Gender = sample(c("F","M"), size = 50, replace = TRUE))

data2 <- data.frame(Genotype = c("zDC.Cre","Villin.Cre","Villin.Cre","zDC.Cre","K14.CreER","Rosa.TSLP","Rosa.TSLP","K14.CreER"), 
                    Litter_ID = c("B23701-2", "B23744-1", "B23744-2", "B23745-2", "B23844-1","B23944-1", "B23944-2", "B23951-1"),
                    PCR_Temp = c("Z","Y","Y","Z","Y","Z","Z","Y"),
                    Rxns = c(1,1,1,1,1,2,2,1))
data <- merge(data1,data2)
data
#   Litter_ID MouseID Gender   Genotype PCR_Temp Rxns
#1   B23701-2   ZP810      F    zDC.Cre        Z    1
#2   B23701-2   ZP992      M    zDC.Cre        Z    1
#3   B23701-2   ZO960      F    zDC.Cre        Z    1
#4   B23744-1   ZO122      F Villin.Cre        Y    1
#5   B23744-1   ZQ259      F Villin.Cre        Y    1
#... 45 more rows

Answered By - Ian Campbell

Answer Checked By - David Marino (PHPFixing Volunteer)