'ind' and 'k' attributes lost while merging (mergeQ)

[konopinski]

Hi,

I love the package so much I made a small pipeline to automatically analyse Structure runs. While plotting I had a small issue with fonts ("font family was not found in Windows database" or so) but solved it with extrafonts package (font_import(), loadfonts()) but this is just to let you and others know as this is more general issue with graphs in R.

My issue is like in title. In the pipeline I wrote the sequence is:
readQ(file, indlabfromfile = TRUE)
alignK()
mergeQ()

The first two commands retain "ind" and "k" attributes but after 'mergeQ' the attributes disappear, which is reported as warning message while plotting (plotQ). It's not a big deal but warnings are disturbing for users and I just wanted to let you know.

Anyway it is possible to add the attributes manually but it's a bit tricky (I cannot find a way to use lapply for that purpose)

MK

[royfrancis]

Hi,
Thanks for the comments. Hmm.. The font issue is supposed to be optional for using external fonts using the extrafonts package. For normal use, it shouldn't matter. When do you get this message "font family was not found in Windows database"?
Thanks for the note on attributes. I will look into that.
Thanks :)

[konopinski]

The pipeline is as follows:

### I did some testing of different Structure setup:
StructDir <- "d:/R/Dzik/Structure/"
projects <- list.dirs(paste0(StructDir),full.names =FALSE,recursive = FALSE)
### Structure file contains all the information in extra columns
### including geo references:
geo <- read.table(file=paste0(StructDir,"project_data"),header = TRUE,
                sep = "\t", stringsAsFactors = FALSE, row.names = 1)[c(2,6,7)]
### and so, all the projects are analysed in this loop:
for (i in projects){
  structFiles <- list.files(path=paste0(StructDir,i,"/Results/"),
                      full.names = TRUE)
  Structs <- pophelper::readQ(files = structFiles, 
                      filetype = "structure", indlabfromfile = TRUE)
  qAligned <- alignK(Structs)
  qTable <- tabulateQ(qAligned)
  qSummary <- summariseQ(qTable)
### To see if everything goes right the summary is exported to a file:
  write.table(qSummary,file=paste0("Summary_",i,".xls"),
                      sep = "\t",quote = FALSE)

  evan <- evannoMethodStructure(qSummary,returnplot = TRUE, 
                      returndata = TRUE, exportplot = TRUE, 
                      outputfilename = paste0("Evanno_",i), imgtype = "pdf",
                      basesize = 6,xaxisbreaks = unique(qTable[,"k"]))
### K is picked automatically. Still I always check the pdf plot
  K = evan$data[which(evan$data[,"deltaK"]==max(evan$data[,"deltaK"],
                      na.rm = TRUE)),"k"]
### In this line the attributes are lost
  qMerged <- mergeQ(qAligned)

### ... so I kick them back in
  for (j in 1:length(qSummary[,1])){
    attr(qMerged[[j]],"ind") <- qSummary[j,"ind"]
    attr(qMerged[[j]],"k") <- qSummary[j,"k"]}

### ... and the plot is...
  plotQ(qMerged[K],imgtype = "pdf", returnplot = TRUE, width = 30, height =6, 
                      outputfilename = paste0("StrBarplot_",i,"_K",K), 
                      grplabsize=3.5, showindlab=FALSE, useindlab = TRUE, 
                      grplab = geo[1], basesize = 15)
}
### so I get the plot in file, while on the screen:
# 
# Drawing plot ...
# StrBarplot_ac_Loc_PI_lamPop_alphPop_metro100_K2.pdf exported.
# $plot
# $plot[[1]]
# TableGrob (4 x 1) "arrange": 2 grobs
#   z     cells    name           grob
# 1 1 (1-3,1-1) arrange gtable[layout]
# 2 2 (4-4,1-1) arrange gtable[layout]
# 
# 
# $data
# $data$qlist
# [1] NA
# 
# $data$grplab
# [1] NA
# 
# 
# Warning message:
# In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
#   rodzina czcionek nie została znaleziona w bazie czcionek systemu Windows
[the font family was not found in Windows database (in Polish ;)]

Does this help?