I am using docker container of too-many-cells v0.1.5.0 for my data. The make-tree is w

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I think I only have ASCII symbols. Below my entire command <div class="snippet-cli

Cannot read draw-leaf error about too-many-cells HOT 7 CLOSED

gregoryschwartz commented on May 29, 2024

Cannot read draw-leaf error

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Comments (7)

ccruizm commented on May 29, 2024

Hello! I am having the same problem

 Cannot read draw-leaf. If using DrawContinuous, remember to put features in a list: DrawItem (DrawContinuous [\"FEATURE\"])
CallStack (from HasCallStack):
  error, called at app/Main.hs:363:36 in main:Main

I used as input a csv but have tried several times and still get the same error

My code:

singularity run too-many-cells make-tree \
    --prior immune_out \
    --matrix-path immune.csv \
    --labels-file labels.celltype_immune.csv \
    --smart-cutoff 1 \
    --min-size 1 \
    --draw-leaf "DrawItem (DrawContinuous [(\"CD14\"), (\"P2RY12\")])" \
    --draw-colors "[\"#e41a1c\", \"#377eb8\", \"#4daf4a\", \"#eaeaea\"]" \
    --draw-scale-saturation 10 \
    --output out_gene_expression \
    > clusters_pruned_immune.csv

Thanks in advance for the help!

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GregorySchwartz commented on May 29, 2024

You have parentheses around each feature in --draw-leaf. Try removing them and re-run the command.

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ccruizm commented on May 29, 2024

Still same problem. Changed to --draw-leaf "DrawItem (DrawContinuous [\"CD14\", \"P2RY12\"])"

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GregorySchwartz commented on May 29, 2024

Could you maybe have Unicode instead of ASCII symbols in your command? Can I see your latest command with the latest error?

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ccruizm commented on May 29, 2024

I think I only have ASCII symbols. Below my entire command

 singularity run too-many-cells m
>     --prior gbm_immune_out \
>     --matrix-path gbm_immune.csv \
>     --labels-file labels.celltype_immune.csv \
>     --smart-cutoff 1 \
>     --min-size 1 \
>     --draw-leaf "DrawItem (DrawContinuous [\"CD14\", \"P2RY12\"])" \
>     --draw-colors "[\"#e41a1c\", \"#377eb8\", \"#4daf4a\", \"#eaeaea\"]" \
>     --draw-scale-saturation 10 \
>     --output out_gene_expression \
>     > clusters_pruned_immune.csv
Planning leaf colors [=====>..............................................]  10%too-many-cells: Cannot read draw-leaf. If using DrawContinuous, remember to put features in a list: DrawItem (DrawContinuous [\"FEATURE\"])
CallStack (from HasCallStack):
  error, called at app/Main.hs:363:36 in main:Main

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GregorySchwartz commented on May 29, 2024

This looks fine... What if you put the string in single quotes with normal unescaped quotation marks for the features?

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GregorySchwartz commented on May 29, 2024

How did you make the singularity image? What version of the docker?

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