showRaw() not working when rows argument is vector containing row names

[ellisifnygaard]

When I use showRaw() with a rows argument consisting of a vector containing row names, I get the following error:

Error in dimnames(x) <- dn :
length of 'dimnames' [1] not equal to array extent

Running traceback() results in:

2: rownames<- (*tmp*, value = data_summary$rownames[rows])

It appears to stem from this line:
https://github.com/jromanowska/HaplinMethyl/blob/7fc4afdc0c45f38321896fb55323bf1d54dc9372/R/showRaw.R#L98C50-L98C54

There are no issues when rows is integers, or when columns is integers or a vector with column names.

Perhaps rownames(show_matrix) <- data_summary$rownames[rows] should be replaced by an if-else statement conditional on whether all(is.character(rows)) is TRUE or FALSE. If TRUE, use rownames(show_matrix) <- rows, and if FALSE, then use rownames(show_matrix) <- data_summary$rownames[rows].

[ellisifnygaard]

It looks like the problem might stem from how Haplin's internal f.get.gen.data.cols() works, which is used on line 86. It returns an ff_matrix that has column names, but no row names.
https://github.com/cran/Haplin/blob/8bb309fc06002300850c4cf0a2237867e39eae69/R/f.get.gen.data.cols.R

It makes sense for Haplin:::f.get.gen.data.cols() to do this, considering that the ff reference manual states that

It is recommended not to assign row.names to a large ffdf object.

and I assume this may apply to ff objects as well.

@jromanowska I'm guessing that it is simpler and faster to make changes to functions in HaplinMethyl rather than make changes to Haplin, so perhaps we should either

1. tweak showRaw so that it can manage to select rows when the user supplies a vector with row names (if possible - I can't think of a specific solution at present), or
2. change the documentation/description of showRaw to state that you have to use row numbers when extracting particular rows and not row names.

[ellisifnygaard]

I have now done some tweaks locally so that I can use showRaw in one of preprocessing stages of the pipeline that I'm developing.

I customised Haplin:::f.get.gen.data.cols() so that it is capable of returning an ff_matrix with row names when desirable instead of just column names. I added an argument called include.rownames.

In showRaw, I commented out line 98,

rownames(show_matrix) <- data_summary$rownames[rows] ,

so that the function does not break when rows is a vector with row names/CpG IDs.

Let me know if you would like this fix implemented in Haplin and HaplinMethyl. Alternatively (if it is all right in terms of copyright), we can fix this bug without requiring changes to be made to the Haplin package by adding my customised version of Haplin:::f.get.gen.data.cols() as an internal function in HaplinMethyl.

[jromanowska]

We need to wait for the new Haplin release to be able to fix that... :-/