Getter and setters #484

Daenarys8 · 2024-01-25T01:57:52Z

TuomasBorman

Looks good. Now add also .add_values_to_reducedDim and other .add* methods when the returned value is TreeSUmmairzedExperiment and the value is added to colData/rowData, reducedDim...

Also, there are lots of lines where only spaces are removed. Can you revert those changes? It is really hard to keep up with what has changed now. (I know what is done, but it is super hard for user...)

TuomasBorman · 2024-01-25T19:21:01Z

R/agglomerate.R

-        empty.fields = c(NA, "", " ", "\t", "-", "_"), ...){
+        empty.fields = c(NA, "", " ", "\t", "-", "_"), altexp = NULL, ...){
        # input check


There should not be reason for adding altexp parameter. It should be passed with ...

I will get back to this tomorrow. This is little bit more complicated thing.

Because we have to allow MARGIN and altExp. It might be necessary to work with the components of TreeSE instead of the whole TreeSE.

Meaning that:

First fetch rowData, tree, assays...

agglomerate values

Add values back to TreeSE

Or then we can just create another function for MARGIN = 2

Currently, we do not have use for agglomerating data column-wise but there might be in the future...

I can make a suggestion of this. I have to try different approaches and let's discuss about this after that

TuomasBorman · 2024-01-25T19:23:58Z

R/utils.R

-}
-
-.is_a_string <- function(x){
-  is.character(x) && length(x) == 1L
-}
-
-.is_an_integer <- function(x){
-    is.numeric(x) && length(x) == 1L && x%%1==0
-}
-
-.are_whole_numbers <- function(x){
-  tol <- 100 * .Machine$double.eps
-  abs(x - round(x)) <= tol && !is.infinite(x)
-}
-
-.is_numeric_string <- function(x){
-  x <- as.character(x)
-  suppressWarnings({x <- as.numeric(x)})
-  !is.na(x)
-}
-
-.is_function <- function(x){
-  typeof(x) == "closure" && is(x, "function")
-}
-


Why it seems that all these functions have changed

Oh its because to run GHA, I put commits against mia:master. So it includes all the earlier commits you pushed in getter_and_setters

These lines have not changed in my branch. Would it be possible if you make changes directly to mia (without using fork). I can give you an access if you have not already

okay. I don't have access.

TuomasBorman · 2024-01-25T19:31:16Z

R/calculateOverlap.R

-          sample1 <- assay[ , sample_pair[1]]
-          sample2 <- assay[ , sample_pair[2]]


You could just use variable name "assay" so it does not look that everything has changed

TuomasBorman · 2024-01-25T19:33:39Z

R/cluster.R

-    if (length(MARGIN) != 1L 
-        || !(MARGIN %in% c(1, 2, "features", "samples", "columns", 


There is lots of removed spaces. It is good that there is no empty spaces, but it looks like these all lines have changed, so it is better to not remove those spaces

TuomasBorman · 2024-01-25T19:44:20Z

So to summarize: it is better to modify only those lines where it is relevant. You can do another PR for removing additional spaces if we see that necessary

TuomasBorman · 2024-02-01T08:07:20Z

Hello!

Sorry that it took so long. I made changes to mia:getters_and_setters branch. Please see those. They are related to agglomerateByRank function. Now, MARGIN is supported meaning that we can utilize this function also to columns (altexp was already working...).

devtools::load_all()

data("GlobalPatterns")

tse <- GlobalPatterns

# Agglomerate to all ranks
altExps(tse) <- splitByRanks(tse)

# Agglomerate altExp
altExp(tse, "test") <- tse[1:10, ]
tse_altExp <- agglomerateByRank(tse, rank = "Kingdom", altexp = "test")
tse_altExp

# Create ranks for columns
colData(tse)[["Kingdom"]] <- sample(c("king1", "king2", "king3"), size = ncol(tse), replace = TRUE)
colData(tse)[["Class"]] <- sample(c("class1"), size = ncol(tse), replace = TRUE)
colData(tse)[["Species"]] <- sample(c("species1", "species2", "species3", "species4"), size = ncol(tse), replace = TRUE)
colData(tse)

# Agglomerate columns
tse_col <- agglomerateByRank(tse, rank = "Kingdom", MARGIN = 2)
tse_col

tse_col <- agglomerateByRank(tse, rank = "Class", MARGIN = 2)
colData(tse_col)

Can you give feedback on that? Is there anything that could break? Is it too complex solution / is it easy to follow what happens? If everything is good, I think we can proceed again.

antagomir · 2024-03-07T11:43:52Z

@Daenarys8 any chance to resolve the conflicts and finalize this one?

Daenarys8 · 2024-03-08T02:11:46Z

ACK. Will push an update asap.

Signed-off-by: Daenarys8 <[email protected]>

antagomir · 2024-06-26T12:11:06Z

This is old PR, still open. What's the status of this one @Daenarys8 ?

TuomasBorman · 2024-06-26T12:15:29Z

This might be something that we should check in the future, not now. This would be good addition, but requires lots of work and I am not sure if it is worth to do at least now when we have other tasks

antagomir · 2024-06-26T12:17:29Z

Ok. I was just worried about having too many active open PRs.

TuomasBorman · 2024-07-02T09:20:02Z

Closing for now

TuomasBorman added 7 commits December 13, 2023 13:37

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TuomasBorman requested changes Jan 25, 2024

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Daenarys8 force-pushed the getter_and_setters branch 9 times, most recently from f25b8fa to 4f31b15 Compare March 11, 2024 15:28

1-microbiome#480

2b5a337

Signed-off-by: Daenarys8 <[email protected]>

Daenarys8 force-pushed the getter_and_setters branch from 4f31b15 to 2b5a337 Compare March 11, 2024 15:33

TuomasBorman mentioned this pull request May 12, 2024

Get top explanatory features from PCoA loadings #541

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TuomasBorman closed this Jul 2, 2024

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Getter and setters #484

Getter and setters #484

Daenarys8 commented Jan 25, 2024 •

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		sample1 <- assay[ , sample_pair[1]]
		sample2 <- assay[ , sample_pair[2]]

		if (length(MARGIN) != 1L
		\|\| !(MARGIN %in% c(1, 2, "features", "samples", "columns",

Getter and setters #484

Getter and setters #484

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Daenarys8 commented Jan 25, 2024 • edited Loading

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TuomasBorman commented Jan 25, 2024

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Daenarys8 commented Jan 25, 2024 •

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