generateCurves Creates an Empty Result

[DarioS]

An list of NULLs is returned by a call to generateCurves function, so lisa function can't set row names on it.

Browse[1]> head(cellSummary)
SplitDataFrameList of length 6
$`1`
DataFrame with 1625 rows and 6 columns
      imageID      cellID imageCellID         x         y               cellType
     <factor> <character> <character> <numeric> <numeric>            <character>
1           1 cell_358130         1_1    49.000   1.05263                  HER2+
2           1 cell_358131         1_2   345.000   3.92308         HR- CKlow CK5+
3           1 cell_358132         1_3    29.500   5.00000      Fibroblasts CD68+
4           1 cell_358133         1_4   291.192   4.88462 Macrophages Vim+ CD4..
5           1 cell_358134         1_5   261.254   4.29851 Macrophages Vim+ Slug+
...       ...         ...         ...       ...       ...                    ...
1621        1 cell_359750      1_1621   383.965   502.807 Macrophages Vim+ Slug-
1622        1 cell_359751      1_1622   304.675   502.725 Macrophages Vim+ CD4..
1623        1 cell_359752      1_1623   404.263   501.800          Myoepithelial
1624        1 cell_359753      1_1624   464.870   502.522 Macrophages Vim+ Slug-
1625        1 cell_359754      1_1625   394.486   502.486          Myoepithelial

...
<5 more elements>
Browse[1]> fast
  FALSE
Browse[1]> str(generateCurves)
function (data, Rs, window, window.length, BPcellType = BPcellType, sigma = sigma, ...)  
Browse[1]> Rs
  20  50 100
Browse[1]> window
  "convex"
Browse[1]> window.length
NULL
Browse[1]> sigma
  50
Browse[1]> curveList <- BiocParallel::bplapply(cellSummary, generateCurves, 
        Rs = Rs, window = window, window.length = window.length, 
        BPcellType = BPcellType, BPPARAM = BPimage, sigma = sigma)
Browse[1]> head(curveList, 3)
$`1`
NULL
$`3`
NULL
$`4`
NULL

Browse[1]>   rownames(curves) <- as.character(unlist(lapply(cellSummary, function(x) x$cellID)))
  Error in dimnames(x) <- dn: length of 'dimnames' [1] not equal to array extent

Traceback.

1: lisaClust(IMC, k = 10, sigma = 50, BPPARAM = MulticoreParam(16), fast = FALSE, 
2: lisa(cd, Rs = Rs, BPPARAM = BPPARAM, window = window, window.length = window.le
3: `rownames<-`(`*tmp*`, value = as.character(unlist(lapply(cellSummary, function(

[ellispatrick]

Hi Dario, Did you set fast = FALSE or is that the default? This needs to be depreciated. Get Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Dario Strbenac ***@***.***> Sent: Monday, July 29, 2024 6:00:32 PM To: SydneyBioX/lisaClust ***@***.***> Cc: Subscribed ***@***.***> Subject: [SydneyBioX/lisaClust] generateCurves Creates an Empty Result (Issue #9) An list of NULLs is returned by a call to generateCurves function, so lisa function can't set row names on it. Browse[1]> head(cellSummary) SplitDataFrameList of length 6 $`1` DataFrame with 1625 rows and 6 columns imageID cellID imageCellID x y cellType <factor> <character> <character> <numeric> <numeric> <character> 1 1 cell_358130 1_1 49.000 1.05263 HER2+ 2 1 cell_358131 1_2 345.000 3.92308 HR- CKlow CK5+ 3 1 cell_358132 1_3 29.500 5.00000 Fibroblasts CD68+ 4 1 cell_358133 1_4 291.192 4.88462 Macrophages Vim+ CD4.. 5 1 cell_358134 1_5 261.254 4.29851 Macrophages Vim+ Slug+ ... ... ... ... ... ... ... 1621 1 cell_359750 1_1621 383.965 502.807 Macrophages Vim+ Slug- 1622 1 cell_359751 1_1622 304.675 502.725 Macrophages Vim+ CD4.. 1623 1 cell_359752 1_1623 404.263 501.800 Myoepithelial 1624 1 cell_359753 1_1624 464.870 502.522 Macrophages Vim+ Slug- 1625 1 cell_359754 1_1625 394.486 502.486 Myoepithelial ... <5 more elements> Browse[1]> fast FALSE Browse[1]> str(generateCurves) function (data, Rs, window, window.length, BPcellType = BPcellType, sigma = sigma, ...) Browse[1]> Rs 20 50 100 Browse[1]> window "convex" Browse[1]> window.length NULL Browse[1]> sigma 50 Browse[1]> curveList <- BiocParallel::bplapply(cellSummary, generateCurves, Rs = Rs, window = window, window.length = window.length, BPcellType = BPcellType, BPPARAM = BPimage, sigma = sigma) Browse[1]> head(curveList, 3) $`1` NULL $`3` NULL $`4` NULL Browse[1]> rownames(curves) <- as.character(unlist(lapply(cellSummary, function(x) x$cellID))) Error in dimnames(x) <- dn: length of 'dimnames' [1] not equal to array extent Traceback. 1: lisaClust(IMC, k = 10, sigma = 50, BPPARAM = MulticoreParam(16), fast = FALSE, 2: lisa(cd, Rs = Rs, BPPARAM = BPPARAM, window = window, window.length = window.le 3: `rownames<-`(`*tmp*`, value = as.character(unlist(lapply(cellSummary, function( — Reply to this email directly, view it on GitHub<#9>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACAALBKAVBUVHQAKXP4QL2LZOXZCBAVCNFSM6AAAAABLTXEBKWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQZTINZSHEZTGNQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[DarioS]

I chose it but I shall leave it at default in future until it is made defunct.