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paiva-s-lab / FlowCT

FlowCT: A semi-automated workflow for deconvolution of immunophenotypic data and objective reporting on large datasets
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Heatmap functions not working #14

Closed Rhubarbcream closed 7 months ago

Rhubarbcream commented 7 months ago

When running

> median.heatmap(fcs, assay.i = "transformed", not.metadata = c("sample_id", "filename"))

R displays:

error in med[, markers.to.use] : subscript out of bounds

Unfortunately it does not help transposing the matrix in assay(fcs)... Are there other options?

jgarces02 commented 7 months ago

Hi. Could you show me the markers you're using, please?

On Sun, Jan 7, 2024, 2:38 PM Rhubarbcream @.***> wrote:

When running

median.heatmap(fcs, assay.i = "transformed", not.metadata = c("sample_id", "filename"))

R displays:

error in med[, markers.to.use] : subscript out of bounds

Unfortunately it does not help transposing the matrix in assay(fcs)... Are there other options?

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Rhubarbcream commented 7 months ago

Yes, sure:

> row.names(assay(fcs))
 [1] "FSC-A"  "FSC-H"  "FSC-W"  "SSC-A"  "SSC-H"  "SSC-W"  "CD19"   "FoxP3"  "CD45-2" "CD4"    "CD11b"  "CD8"   
[13] "F4/80"  "Ly-6C"  "CD11c"  "CD3"    "CD44"   "D/L"    "CD25"   "CD45-1" "CD62L"  "TNFa"   "RORyt"  "H2D-d" 
[25] "H2D-b"  "VLA-4"  "IFNy"   "Il-6"

These are the markers I would like to use.

jgarces02 commented 7 months ago

Have you corrected them with marker.names()? R cannot deal with hyphens or another special characters.

Also, try to do intersect(rownames(fcs), c("your", "makers", "of", "interest")) and see what is the maker giving problems... the error is for something not matching.

On Sun, Jan 7, 2024, 4:19 PM Rhubarbcream @.***> wrote:

Yes, sure:

row.names(assay(fcs)) [1] "FSC-A" "FSC-H" "FSC-W" "SSC-A" "SSC-H" "SSC-W" "CD19" "FoxP3" "CD45-2" "CD4" "CD11b" "CD8" [13] "F4/80" "Ly-6C" "CD11c" "CD3" "CD44" "D/L" "CD25" "CD45-1" "CD62L" "TNFa" "RORyt" "H2D-d" [25] "H2D-b" "VLA-4" "IFNy" "Il-6"

These are the markers I would like to use.

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Rhubarbcream commented 7 months ago

Thank you for the suggestion, I changed the marker names and it worked! Sometimes it's the little things that bring joy :)