Yunuuuu
commented
8 months ago And the differences were large.
Closed Yunuuuu closed 7 months ago
Yunuuuu
commented
8 months ago And the differences were large.
bnprks
commented
8 months ago The rank_transform function has documented differences from the colRanks function:
Rank values are offset such that the rank of a 0 value is 0, and ties are handled by averaging ranks.
If you account for this in your test, you should find that all the values match up:
zero_rank <- matrixStats::colMins(mat)
obj <- as.matrix(obj)
dimnames(obj) <- NULL
waldo::compare(BPCells::add_cols(as.matrix(obj), zero_rank), mat)Note that the method I showed for finding the zero_rank assumes that you don't have negative values in the input matrix, but the BPCells function should still work properly even in the presence of negative input values.
Edit: to clarify the rationale here -- maintaining sparse matrices in BPCells is important for efficiency, which is why rank_transform performs the offset so that the rank of 0 values stays at 0. This doesn't affect most downstream use-cases like spearman correlation or Wilcoxon rank-sum tests. But also, rank_transform is not itself an exported function from BPCells due to this somewhat unusual behavior.
Yunuuuu
commented
8 months ago Thanks for the explanations, is it possible to provide an argument to control the behaviour, so we can implement a rowRanks and colRanks function easily
Yunuuuu
commented
8 months ago Or implement a colMins function, so can combine both function to create rowRanks and colRanks function
bnprks
commented
8 months ago Hey @Yunuuuu, thanks for taking a look this and the other issues/pull requests you've opened this weekend -- I appreciate the help! It will take me a little bit of time to review each of the issues and pull requests, probably Tuesday/Wednesday for most of them since I'm a bit busy for the start of this week.
Do you happen to know any C++? I think implementing a colMins function might be the cleanest way to get at your use-case. It's not on my immediate roadmap, but it could make a good first contribution to the C++ side of the code base and would help you solve your use-case here. I can of course offer pointers if you're interested, or even arrange a short video call in Pacific Time to give an overview of all the steps.
Yunuuuu
commented
8 months ago Thanks for your great work in this package, I can only write some small C++ codes. I have tried to understand the function matrix_value_histogram_cpp and wilcoxon_rank_sum, they are too complicated for me. I'm not famaliar many basic cpp function.
These issues were all found when I tested the BPCells basic function,I think I can make a pull request to add more unit tests
bnprks
commented
8 months ago Hi @Yunuuuu, I think I've come up with a way you can do this fully with the existing BPCells functionality. I still think that the performance of an exact colRanks equivalent in BPCells is likely to be quite poor since the matrix will be dense thus requiring 10-20x more computation and storage for downstream operations than the sparse version that BPCells provides.
However, if you really want to implement this operation for compatibility reasons, then I think this should do the trick for you:
dense_col_rank <- function(m) {
zeros <- nrow(m) - matrix_stats(m, col_stats="nonzero")$col_stats["nonzero",]
negatives <- nrow(m) - colSums(m > 0) - zeros
rank_offsets <- ifelse(zeros != 0, negatives + (1+zeros)/2, 0)
add_cols(rank_transform(m, "col"), rank_offsets)
}Sorry for the delayed reply, by following the code snippet you provided, I successfully created the rowRanks and colRanks function. For me, it's okay to close this thread or you would lik to keep it open for others who might have similar questions.
I just added the modified rank_transform for others who may want to use it:
rank_transform <- function(object, axis = NULL, offset = TRUE, ...) {
main_axis <- BPCells::storage_order(object)
if (is.null(axis)) {
axis <- main_axis
cli::cli_inform("Doing {.val {axis}} rank transformation")
} else {
axis <- match.arg(axis, c("row", "col"))
if (axis != main_axis) {
cli::cli_warn(c(
"transposing the storage order for {.arg object}",
i = "{.arg axis} specified is different from the the storage axis of {.arg object} ({.val {main_axis}})" # nolint
))
object <- BPCells::transpose_storage_order(
matrix = object, ...
)
}
}
matrix <- BPCells:::rank_transform(mat = object, axis = axis)
if (!offset) {
if (axis == "row") {
nonzero <- BPCells::matrix_stats(object,
row_stats = "nonzero"
)$row_stats["nonzero", , drop = TRUE]
zeros <- ncol(object) - nonzero
negatives <- ncol(object) - rowSums(object > 0) - zeros
rank_offsets <- ifelse(zeros != 0,
negatives + (1 + zeros) / 2, 0
)
matrix <- matrix + rank_offsets
} else {
nonzero <- BPCells::matrix_stats(object,
col_stats = "nonzero"
)$col_stats["nonzero", , drop = TRUE]
zeros <- nrow(object) - nonzero
negatives <- nrow(object) - colSums(object > 0) - zeros
rank_offsets <- ifelse(zeros != 0,
negatives + (1 + zeros) / 2, 0
)
matrix <- t(t(matrix) + rank_offsets)
}
}
matrix
}
Glad it worked for you, and thanks for sharing that code snippet
Created on 2024-01-28 with reprex v2.0.2