check this example:
> a = matrix(1:9, nrow = 3, ncol = 3, dimnames = list(LETTERS[1:3], LETTERS[1:3]))
> a
A B C
A 1 4 7
B 2 5 8
C 3 6 9
the table displays correctly. There are two different ways of writing it to file...
write.csv(a, 'a.csv')
which gives as expected:
"","A","B","C"
"A",1,4,7
"B",2,5,8
"C",3,6,9
and write.table(a, 'a.txt')
which screws up
"A" "B" "C"
"A" 1 4 7
"B" 2 5 8
"C" 3 6 9
indeed, an empty tab is missing.... which is a pain in the butt for downstream things.
Is this a bug or a feature?
Is there a workaround? (other than write.table(cbind(rownames(a), a), 'a.txt', row.names=FALSE
)
Cheers开发者_高级运维, yannick
Citing ?write.table
, section CSV files:
By default there is no column name for a column of row names. If
col.names = NA
androw.names = TRUE
a blank column name is added, which is the convention used for CSV files to be read by spreadsheets.
So you must do
write.table(a, 'a.txt', col.names=NA)
and you get
"" "A" "B" "C"
"A" 1 4 7
"B" 2 5 8
"C" 3 6 9
A slight modification to @Marek very helpful answer WILL add a header to the rownames column: temporarily add the rownames as the first column in the data.frame, and write that, ignoring the real rownames.
> a = matrix(1:9, nrow = 3, ncol = 3, dimnames = list(LETTERS[1:3], LETTERS[1:3]))
> write.table(data.frame("H"=rownames(a),a),"a.txt", row.names=FALSE)
and you get
"H" "A" "B" "C"
"A" 1 4 7
"B" 2 5 8
"C" 3 6 9
For anyone working in the tidyverse (dplyr, etc.), the rownames_to_column()
function from the tibble package can be used to easily convert row.names to a column, e.g.:
library('tibble')
a = as.data.frame(matrix(1:9, nrow=3, ncol=3,
dimnames=list(LETTERS[1:3], LETTERS[1:3])))
a %>% rownames_to_column('my_id')
my_id A B C
1 A 1 4 7
2 B 2 5 8
3 C 3 6 9
Combining this with the row.names=FALSE
option in write.table()
results in output with header names for all columns.
For those who experience the same issue when saving a matrix with write.table()
and want to keep the row.names column, there is actually an extremely simple solution:
write.table(matrix,file="file.csv",quote=F,sep=";", row.names=T
col.names=c("row_name_col;val1_col","val2_col"))
By doing that you're basically tricking the write.table
function into creating a header label for the row.names column. The resulting .csv file would look like this:
row_name_col;val1_col;val2_col
row1;1;4
row2;2;5
row3;3;6
I revised a simple function from @mnel, which adds flexibility by using connections. Here is the function:
my.write <- function(x, file, header, f = write.csv, ...){
# create and open the file connection
datafile <- file(file, open = 'wt')
# close on exit
on.exit(close(datafile))
# if a header is defined, write it to the file (@CarlWitthoft's suggestion)
if(!missing(header)) {
writeLines(header,con=datafile, sep='\t')
writeLines('', con=datafile, sep='\n')
}
# write the file using the defined function and required addition arguments
f(x, datafile,...)
}
You can specify the function to be 'write.table', 'write.csv', 'write.delim' etc.
Cheers!
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