PCR plates work on a coordinate system similar to an X-Y coordinate system. I would like to convert a 96-well PCR plate from this X-Y coordinate system (row and column format) to a single column only format, combining the x-y system together (i.e Row B and Column 12 = B12).
The first dataset provided below, called "pcr_plate", is the format of a 96-well PCR plate.
The second dataset, called "sample_transposed_plate" is an example of the desired outcome.
I've tried classical approaches to transposing data, using code from the follwing packages:
library(dplyr) library(tidyr)
In addition to transform(data.frame, ... )
However, I am confused how to write a code that starts from Row A column 1:12, followed by Row B column 1:12, etc.. while keeping the respective sample (aka well) in an adjacent column
two sample working data sets:
pcr_plate <- read.table ("https://pastebin.com/raw/bGhzj5dU", header = T, sep = "")
sample_transposed_plate <- read.table ("https://pastebin.com/raw/xyzv9cvH", header=T, sep = "") # example of desired outcome
Logically, given there are 96-wells, I should have 96 lines of data in the end (97 with a header). First column would be "location", and second column would be "sample"
You can just use a typical gather to convert from wide to long data:
library(tidyverse)
pcr_plate <- read.table ("https://pastebin.com/raw/bGhzj5dU", header = T, sep = "")
sample_transposed_plate <- read.table ("https://pastebin.com/raw/xyzv9cvH", header=T, sep = "")
pcr_plate_long = pcr_plate %>%
gather(number, content, -pcr.plate) %>%
mutate(number = str_remove(number, "^X"),
well_ID = paste0(pcr.plate, number)) %>%
select(content, well_ID)