Cannot read draw-leaf error

[vswarup]

I am using docker container of too-many-cells v0.1.5.0 for my data. The make-tree is working fine and I am happy with the results, but the gene-expression draw-tree is giving "draw-leaf error" for any gene.
For example in the code below I am trying to plot the expression of MBP gene which is expressed in the data and which is in column 1 of the genes.tsv file (only 1 gene-name column). The path of "priors", matrix file as well as labels are all accurate, but I still do not understand the error. I have also run without "--draw-scale-saturation 10" parameter and getting the same error.

Here is the error

Planning leaf colors [=====>..............................................] 10%too-many-cells: Cannot read draw-leaf.
CallStack (from HasCallStack):
error, called at app/Main.hs:329:36 in main:Main

Here is the code that I am running

docker run -v $INPATH:/data gregoryschwartz/too-many-cells:0.1.5.0 make-tree \ --prior /data/snRNAseq_Processed_AD2019/out_cellType \ --matrix-path /data/snRNAseq_Processed_AD2019 \ --labels-file /data/snRNAseq_Processed_AD2019/labels_CellType.csv \ --draw-leaf "DrawItem (DrawContinuous [\"MBP\"])" \ --draw-scale-saturation 10 \ --output /data/snRNAseq_Processed_AD2019/out_gene_expression \ > ${INPATH}/snRNAseq_Processed_AD2019/clusters_cellType_Expr_pruned.csv

[ccruizm]

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!

[GregorySchwartz]

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

[ccruizm]

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

[GregorySchwartz]

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

[ccruizm]

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

[GregorySchwartz]

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

[GregorySchwartz]

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