Hi, I am trying to plot a frame set using ggycto and autoplot but also to rearrange the frames in a specific order.

I first created a vector with the sample names and then created a matrix that will show the order of the frames in the plot. I use a vector becuase I need to for another loop I have in my script, and I truncate it to 49 for another reason unrelated to this question.

# Create a 96 well plate name spece in a vector
wholeplate <- vector()
rowsinplate <- c("A","B","C","D","E","F","G","H")
for (i in rowsinplate){
  for (j in 1:12){
    wholeplate <- c(wholeplate,paste(i, j, sep=""))
  }
}

ndataset <- vector()
ndataset <- wholeplate[0:49]
#for a later use, make a matrix with 12 columns to store all sample names
layoutmtrx <- matrix(ndataset,ncol = 6, byrow=TRUE)
layoutmtrx

Plotting the frameset with autoplot works fine:
autoplot(fs, "RED.B.HLin", "FSC.HLin", bins=132) + 
  ggcyto_par_set(limits = "data")

But the frames are ordered as they were files names (A1, A10, A11, A12, A2 ...) So I try using ggcyto_arrange either with the matrix order or just changing the number of rows, but I get the same error:

ggcyto_arrange(autoplot(gs[[1]], "RED.B.HLin", "FSC.HLin", bins=132),layout_matrix = layoutmtrx)
ggcyto_arrange(autoplot(fs, "RED.B.HLin", "FSC.HLin", bins=132), nrow=2)

Error in as.ggplot(p) : object 'name' not found

Should I use another function to re-arrange the plots?

autoplot was meant for the most common quick-view plotting operations, for the most part handling the layout for you. To do what you're trying to do (plots by plate well location), you should probably be working through the more flexible ggcyto method. So something like this:

# Using cytoset
cs <- load_cytoset_from_fcs(fcs_path)
rows <- toupper(letters)[1:8]
cols <- 1:12
wholeplate <- cbind(row=rep(rows, each = 12), column=rep(cols, 8))
pd <- pData(cs)
pData(cs) <- cbind(pd, wholeplate)
ggcyto(cs, aes("B710-A", "R660-A")) +
  geom_hex(bins=132) +
  facet_grid(row ~ column)

or, if you're using ncdfFlow because you're still using Bioconductor 3.10:

# Using ncdfFlowSet
fs <- read.ncdfFlowSet(list.files(fcs_path, pattern = "CytoTrol", full.names = TRUE))
rows <- toupper(letters)[1:8]
cols <- 1:12
wholeplate <- cbind(row=rep(rows, each = 12), column=rep(cols, 8))
pd <- pData(fs)
pData(fs) <- cbind(pd, wholeplate)
ggcyto(fs, aes("B710-A", "R660-A")) +
  geom_hex(bins=132) +
  facet_grid(row ~ column)

Of course, you could use a subset of the 96 (in your case, 49) and there's nothing saying you have to lay out the rows and columns as I did there, but hopefully that illustrates the idea. Just use facet_grid (like you would with ggplot). You can use any column available in the pData attached to the cytoset/flowSet/ncdfFlowSet/GatingSet for faceting.