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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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Error in "colors = color_clusters" #5

Closed Weide12 closed 8 months ago

Weide12 commented 1 year ago

Can not find object "colors = color_clusters"

jgarces02 commented 1 year ago

Hi @Weide12. I guess you are following the tutorial... color_clusters is a variable you must create, it's not predefined within.

It's a vector with a length equal to your number of clusters:

color_cluster <- c("red", "black", "green", ...) (and so on until have so many as clusters you have)

Weide12 commented 1 year ago

Thanks jgarces. This helped me. I still have some issues: 1, when run my 20 color data, "qc.and.removeDoublets" report "can not allocate 1535Gb vector"; 2, "dr.plotting" Error in melt.data.table(as.data.table(drmd), measure.vars = no.omit.markers, : 'measure.vars' one or more value is invalid; 3, in heatmap plot can i order the column by condition or patient_id. Thanks. image

jgarces02 commented 1 year ago

I'm glad you solved this problem.

  1. That's not a new problem... it's related to RAM memory and at this time, I cannot find any solution yet. Could you use a computer with more RAM?
  2. With so little information I cannot see what's happening, sorry. Please, check if you're indicating correct names in omit.markers options.
  3. There's no implemented option in the function yet but try to order your matrix before running this function and use clustering.method = NULL.
mlorenzm commented 1 year ago

Regarding your second question, I already faced that problem, when you do not specify color.byon dr.plotting. It has to do with how your markers are named. If you have dashes (i.e. CD3-PE) on your marker names it gives that error

jgarces02 commented 1 year ago

Indeed, @mlorenzm fixed this issue @Weide12. Maybe you can try to install the developmental version?

Weide12 commented 1 year ago

I tried to install the developmental version using this command : devtools::install_github("jgarces02/FlowCT"), it returned an error: Error: Failed to install 'FlowCT' from GitHub: ! System command 'Rcmd.exe' failed

jgarces02 commented 1 year ago

Try: devtools::install_github("paiva-s-lab/FlowCT@develop")

jgarces02 commented 1 year ago

Another option is to change your marker's names to something readable by R, as @mlorenzm indicates.

If you have dashes (i.e. CD3-PE) on your marker names it gives that error