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neurogenomics / MAGMA_Celltyping

Find causal cell-types underlying complex trait genetics
https://neurogenomics.github.io/MAGMA_Celltyping
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Issue in EWCE if I leave MAGMA.Celltyping calculate the quantiles #122

Closed AMCalejandro closed 1 year ago

AMCalejandro commented 2 years ago

So, in the wiki you say image

However, if I do not prepare the quantiles, a specifity_quantile matrix within the ctd object is not generated. Then, EWCE is failing where I am highlighting https://github.com/neurogenomics/MAGMA_Celltyping/blob/8cb235fb495a467fb825819a76b2f154d3840146/R/get_ctd_dendro.r#L25

Example Data Try to plot with and without calculating spec_quantiles

> str(ctAssocsLinear)
List of 7
 $ level1                        :List of 2
  ..$ geneCovarFile: chr "/tmp/Rtmp7tn8CZ/file5ddfd929b060"
  ..$ results      :'data.frame':   24 obs. of  14 variables:
  .. ..$ Celltype      : chr [1:24] "astrocytes_ependymal" "Dopaminergic_Adult" "Dopaminergic_Neuroblast" "Embryonic_Dopaminergic_Neuron" ...
  .. ..$ OBS_GENES     : chr [1:24] "71" "71" "71" "71" ...
  .. ..$ BETA          : num [1:24] -0.005079 -0.004212 -0.000215 0.00292 -0.005705 ...
  .. ..$ BETA_STD      : num [1:24] -0.05943 -0.04793 -0.00273 0.03446 -0.0622 ...
  .. ..$ SE            : num [1:24] 0.00846 0.0085 0.00748 0.0082 0.00951 ...
  .. ..$ P             : num [1:24] 0.725 0.689 0.511 0.362 0.724 ...
  .. ..$ level         : int [1:24] 1 1 1 1 1 1 1 1 1 1 ...
  .. ..$ Method        : chr [1:24] "MAGMA" "MAGMA" "MAGMA" "MAGMA" ...
  .. ..$ GCOV_FILE     : chr [1:24] "educational_attainment.tsv.35UP.10DOWN.level1.MainRun.gsa.out" "educational_attainment.tsv.35UP.10DOWN.level1.MainRun.gsa.out" "educational_attainment.tsv.35UP.10DOWN.level1.MainRun.gsa.out" "educational_attainment.tsv.35UP.10DOWN.level1.MainRun.gsa.out" ...
  .. ..$ CONTROL       : chr [1:24] "BASELINE" "BASELINE" "BASELINE" "BASELINE" ...
  .. ..$ CONTROL_label : chr [1:24] "BASELINE" "BASELINE" "BASELINE" "BASELINE" ...
  .. ..$ log10p        : num [1:24] -0.14 -0.162 -0.291 -0.442 -0.14 ...
  .. ..$ genesOutCOND  : chr [1:24] "NA" "NA" "NA" "NA" ...
  .. ..$ EnrichmentMode: chr [1:24] "Linear" "Linear" "Linear" "Linear" ...
 $ level2                        :List of 2
  ..$ geneCovarFile: chr "/tmp/Rtmp7tn8CZ/file5ddfd3067ed9d"
  ..$ results      :'data.frame':   149 obs. of  14 variables:
  .. ..$ Celltype      : chr [1:149] "Astro1" "Astro2" "CA1Pyr1" "CA1Pyr2" ...
  .. ..$ OBS_GENES     : chr [1:149] "71" "71" "71" "71" ...
  .. ..$ BETA          : num [1:149] -0.001389 -0.002209 0.000956 0.003637 0.003249 ...
  .. ..$ BETA_STD      : num [1:149] -0.0178 -0.0263 0.0111 0.0428 0.0399 ...
  .. ..$ SE            : num [1:149] 0.00825 0.00845 0.00799 0.0082 0.00813 ...
  .. ..$ P             : num [1:149] 0.567 0.603 0.453 0.33 0.346 ...
  .. ..$ level         : int [1:149] 2 2 2 2 2 2 2 2 2 2 ...
  .. ..$ Method        : chr [1:149] "MAGMA" "MAGMA" "MAGMA" "MAGMA" ...
  .. ..$ GCOV_FILE     : chr [1:149] "educational_attainment.tsv.35UP.10DOWN.level2.MainRun.gsa.out" "educational_attainment.tsv.35UP.10DOWN.level2.MainRun.gsa.out" "educational_attainment.tsv.35UP.10DOWN.level2.MainRun.gsa.out" "educational_attainment.tsv.35UP.10DOWN.level2.MainRun.gsa.out" ...
  .. ..$ CONTROL       : chr [1:149] "BASELINE" "BASELINE" "BASELINE" "BASELINE" ...
  .. ..$ CONTROL_label : chr [1:149] "BASELINE" "BASELINE" "BASELINE" "BASELINE" ...
  .. ..$ log10p        : num [1:149] -0.247 -0.22 -0.344 -0.482 -0.461 ...
  .. ..$ genesOutCOND  : chr [1:149] "NA" "NA" "NA" "NA" ...
  .. ..$ EnrichmentMode: chr [1:149] "Linear" "Linear" "Linear" "Linear" ...
 $ total_baseline_tests_performed: num 173
 $ gwas_sumstats_path            : chr "/tmp/Rtmp7tn8CZ/educational_attainment.tsv"
 $ analysis_name                 : chr "MainRun"
 $ upstream_kb                   : num 35
 $ downstream_kb                 : num 10
> str(ctAssocsTop)
List of 7
 $ level1                        :List of 1
  ..$ results:'data.frame': 24 obs. of  14 variables:
  .. ..$ Celltype      : chr [1:24] "astrocytes_ependymal" "Dopaminergic_Adult" "Dopaminergic_Neuroblast" "Embryonic_Dopaminergic_Neuron" ...
  .. ..$ OBS_GENES     : chr [1:24] "71" "71" "71" "71" ...
  .. ..$ BETA          : num [1:24] -0.005079 -0.004212 -0.000215 0.00292 -0.005705 ...
  .. ..$ BETA_STD      : num [1:24] -0.05943 -0.04793 -0.00273 0.03446 -0.0622 ...
  .. ..$ SE            : num [1:24] 0.00846 0.0085 0.00748 0.0082 0.00951 ...
  .. ..$ P             : num [1:24] 0.725 0.689 0.511 0.362 0.724 ...
  .. ..$ level         : int [1:24] 1 1 1 1 1 1 1 1 1 1 ...
  .. ..$ Method        : chr [1:24] "MAGMA" "MAGMA" "MAGMA" "MAGMA" ...
  .. ..$ GCOV_FILE     : chr [1:24] "educational_attainment.tsv.35UP.10DOWN.level1.MainRun.gsa.out" "educational_attainment.tsv.35UP.10DOWN.level1.MainRun.gsa.out" "educational_attainment.tsv.35UP.10DOWN.level1.MainRun.gsa.out" "educational_attainment.tsv.35UP.10DOWN.level1.MainRun.gsa.out" ...
  .. ..$ CONTROL       : chr [1:24] "BASELINE" "BASELINE" "BASELINE" "BASELINE" ...
  .. ..$ CONTROL_label : chr [1:24] "BASELINE" "BASELINE" "BASELINE" "BASELINE" ...
  .. ..$ log10p        : num [1:24] -0.14 -0.162 -0.291 -0.442 -0.14 ...
  .. ..$ genesOutCOND  : chr [1:24] "NA" "NA" "NA" "NA" ...
  .. ..$ EnrichmentMode: chr [1:24] "Top 10%" "Top 10%" "Top 10%" "Top 10%" ...
 $ level2                        :List of 1
  ..$ results:'data.frame': 149 obs. of  14 variables:
  .. ..$ Celltype      : chr [1:149] "Astro1" "Astro2" "CA1Pyr1" "CA1Pyr2" ...
  .. ..$ OBS_GENES     : chr [1:149] "71" "71" "71" "71" ...
  .. ..$ BETA          : num [1:149] -0.001389 -0.002209 0.000956 0.003637 0.003249 ...
  .. ..$ BETA_STD      : num [1:149] -0.0178 -0.0263 0.0111 0.0428 0.0399 ...
  .. ..$ SE            : num [1:149] 0.00825 0.00845 0.00799 0.0082 0.00813 ...
  .. ..$ P             : num [1:149] 0.567 0.603 0.453 0.33 0.346 ...
  .. ..$ level         : int [1:149] 2 2 2 2 2 2 2 2 2 2 ...
  .. ..$ Method        : chr [1:149] "MAGMA" "MAGMA" "MAGMA" "MAGMA" ...
  .. ..$ GCOV_FILE     : chr [1:149] "educational_attainment.tsv.35UP.10DOWN.level2.MainRun.gsa.out" "educational_attainment.tsv.35UP.10DOWN.level2.MainRun.gsa.out" "educational_attainment.tsv.35UP.10DOWN.level2.MainRun.gsa.out" "educational_attainment.tsv.35UP.10DOWN.level2.MainRun.gsa.out" ...
  .. ..$ CONTROL       : chr [1:149] "BASELINE" "BASELINE" "BASELINE" "BASELINE" ...
  .. ..$ CONTROL_label : chr [1:149] "BASELINE" "BASELINE" "BASELINE" "BASELINE" ...
  .. ..$ log10p        : num [1:149] -0.247 -0.22 -0.344 -0.482 -0.461 ...
  .. ..$ genesOutCOND  : chr [1:149] "NA" "NA" "NA" "NA" ...
  .. ..$ EnrichmentMode: chr [1:149] "Top 10%" "Top 10%" "Top 10%" "Top 10%" ...
 $ total_baseline_tests_performed: num 173
 $ gwas_sumstats_path            : chr "/tmp/Rtmp7tn8CZ/educational_attainment.tsv"
 $ analysis_name                 : chr "MainRun"
 $ upstream_kb                   : num 35
 $ downstream_kb                 : num 10

> str(ctd)
List of 2
 $ level1:List of 6
  ..$ specificity :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:296091] 0 1 2 3 4 5 6 7 8 11 ...
  .. .. ..@ p       : int [1:25] 0 12623 25181 35884 47476 60473 72472 85159 96925 110403 ...
  .. .. ..@ Dim     : int [1:2] 14240 24
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : Named chr [1:14240] "ACADM" "ACADVL" "ACAT1" "ACVR1" ...
  .. .. .. .. ..- attr(*, "names")= chr [1:14240] "Acadm" "Acadvl" "Acat1" "Acvr1" ...
  .. .. .. ..$ : chr [1:24] "astrocytes_ependymal" "Dopaminergic_Adult" "Dopaminergic_Neuroblast" "Embryonic_Dopaminergic_Neuron" ...
  .. .. ..@ x       : num [1:296091] 0.0859 0.0907 0.0245 0.0266 0.1668 ...
  .. .. ..@ factors : list()
  ..$ mean_exp    :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:296091] 0 1 2 3 4 5 6 7 8 11 ...
  .. .. ..@ p       : int [1:25] 0 12623 25181 35884 47476 60473 72472 85159 96925 110403 ...
  .. .. ..@ Dim     : int [1:2] 14240 24
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : chr [1:14240] "ACADM" "ACADVL" "ACAT1" "ACVR1" ...
  .. .. .. ..$ : chr [1:24] "astrocytes_ependymal" "Dopaminergic_Adult" "Dopaminergic_Neuroblast" "Embryonic_Dopaminergic_Neuron" ...
  .. .. ..@ x       : num [1:296091] 1.377 1.34 1.314 0.176 0.044 ...
  .. .. ..@ factors : list()
  ..$ annot       :'data.frame':    24 obs. of  1 variable:
  .. ..$ celltype: chr [1:24] "astrocytes_ependymal" "Dopaminergic Adult" "Dopaminergic Neuroblast" "Embryonic Dopaminergic Neuron" ...
  ..$ standardised: logi TRUE
  ..$ species     :List of 2
  .. ..$ input_species : chr "mouse"
  .. ..$ output_species: chr "human"
  ..$ versions    :List of 3
  .. ..$ EWCE      :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:3] 1 5 5
  .. ..$ orthogene :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:3] 1 3 1
  .. ..$ homologene:Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:6] 1 4 68 19 3 27
 $ level2:List of 6
  ..$ specificity :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:1494549] 0 1 2 3 4 5 6 7 8 11 ...
  .. .. ..@ p       : int [1:150] 0 11070 22299 35820 49231 60945 72757 81515 89851 101568 ...
  .. .. ..@ Dim     : int [1:2] 14240 149
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : Named chr [1:14240] "ACADM" "ACADVL" "ACAT1" "ACVR1" ...
  .. .. .. .. ..- attr(*, "names")= chr [1:14240] "Acadm" "Acadvl" "Acat1" "Acvr1" ...
  .. .. .. ..$ : chr [1:149] "Astro1" "Astro2" "CA1Pyr1" "CA1Pyr2" ...
  .. .. ..@ x       : num [1:1494549] 0.01329 0.01375 0.00448 0.00389 0.09232 ...
  .. .. ..@ factors : list()
  ..$ mean_exp    :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:1494549] 0 1 2 3 4 5 6 7 8 11 ...
  .. .. ..@ p       : int [1:150] 0 11070 22299 35820 49231 60945 72757 81515 89851 101568 ...
  .. .. ..@ Dim     : int [1:2] 14240 149
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : chr [1:14240] "ACADM" "ACADVL" "ACAT1" "ACVR1" ...
  .. .. .. ..$ : chr [1:149] "Astro1" "Astro2" "CA1Pyr1" "CA1Pyr2" ...
  .. .. ..@ x       : num [1:1494549] 1.265 1.544 1.588 0.162 0.103 ...
  .. .. ..@ factors : list()
  ..$ annot       :'data.frame':    149 obs. of  1 variable:
  .. ..$ celltype: chr [1:149] "Astro1" "Astro2" "CA1Pyr1" "CA1Pyr2" ...
  ..$ standardised: logi TRUE
  ..$ species     :List of 2
  .. ..$ input_species : chr "mouse"
  .. ..$ output_species: chr "human"
  ..$ versions    :List of 3
  .. ..$ EWCE      :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:3] 1 5 5
  .. ..$ orthogene :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:3] 1 3 1
  .. ..$ homologene:Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:6] 1 4 68 19 3 27

> str(ctd_quant)
List of 2
 $ level1:List of 8
  ..$ specificity          :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:296091] 0 1 2 3 4 5 6 7 8 11 ...
  .. .. ..@ p       : int [1:25] 0 12623 25181 35884 47476 60473 72472 85159 96925 110403 ...
  .. .. ..@ Dim     : int [1:2] 14240 24
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : Named chr [1:14240] "ACADM" "ACADVL" "ACAT1" "ACVR1" ...
  .. .. .. .. ..- attr(*, "names")= chr [1:14240] "Acadm" "Acadvl" "Acat1" "Acvr1" ...
  .. .. .. ..$ : chr [1:24] "astrocytes_ependymal" "Dopaminergic_Adult" "Dopaminergic_Neuroblast" "Embryonic_Dopaminergic_Neuron" ...
  .. .. ..@ x       : num [1:296091] 0.0859 0.0907 0.0245 0.0266 0.1668 ...
  .. .. ..@ factors : list()
  ..$ mean_exp             :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:296091] 0 1 2 3 4 5 6 7 8 11 ...
  .. .. ..@ p       : int [1:25] 0 12623 25181 35884 47476 60473 72472 85159 96925 110403 ...
  .. .. ..@ Dim     : int [1:2] 14240 24
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : chr [1:14240] "ACADM" "ACADVL" "ACAT1" "ACVR1" ...
  .. .. .. ..$ : chr [1:24] "astrocytes_ependymal" "Dopaminergic_Adult" "Dopaminergic_Neuroblast" "Embryonic_Dopaminergic_Neuron" ...
  .. .. ..@ x       : num [1:296091] 1.377 1.34 1.314 0.176 0.044 ...
  .. .. ..@ factors : list()
  ..$ annot                :'data.frame':   24 obs. of  1 variable:
  .. ..$ celltype: chr [1:24] "astrocytes_ependymal" "Dopaminergic Adult" "Dopaminergic Neuroblast" "Embryonic Dopaminergic Neuron" ...
  ..$ standardised         : logi TRUE
  ..$ species              :List of 2
  .. ..$ input_species : chr "mouse"
  .. ..$ output_species: chr "human"
  ..$ versions             :List of 3
  .. ..$ EWCE      :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:3] 1 5 5
  .. ..$ orthogene :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:3] 1 3 1
  .. ..$ homologene:Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:6] 1 4 68 19 3 27
  ..$ specificity_quantiles:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:296091] 0 1 2 3 4 5 6 7 8 11 ...
  .. .. ..@ p       : int [1:25] 0 12623 25181 35884 47476 60473 72472 85159 96925 110403 ...
  .. .. ..@ Dim     : int [1:2] 14240 24
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : Named chr [1:14240] "ACADM" "ACADVL" "ACAT1" "ACVR1" ...
  .. .. .. .. ..- attr(*, "names")= chr [1:14240] "Acadm" "Acadvl" "Acat1" "Acvr1" ...
  .. .. .. ..$ : chr [1:24] "astrocytes_ependymal" "Dopaminergic_Adult" "Dopaminergic_Neuroblast" "Embryonic_Dopaminergic_Neuron" ...
  .. .. ..@ x       : num [1:296091] 36 36 22 23 39 14 32 40 25 38 ...
  .. .. ..@ factors : list()
  ..$ specificity_deciles  :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:296091] 0 1 2 3 4 5 6 7 8 11 ...
  .. .. ..@ p       : int [1:25] 0 12623 25181 35884 47476 60473 72472 85159 96925 110403 ...
  .. .. ..@ Dim     : int [1:2] 14240 24
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : Named chr [1:14240] "ACADM" "ACADVL" "ACAT1" "ACVR1" ...
  .. .. .. .. ..- attr(*, "names")= chr [1:14240] "Acadm" "Acadvl" "Acat1" "Acvr1" ...
  .. .. .. ..$ : chr [1:24] "astrocytes_ependymal" "Dopaminergic_Adult" "Dopaminergic_Neuroblast" "Embryonic_Dopaminergic_Neuron" ...
  .. .. ..@ x       : num [1:296091] 9 9 6 6 10 4 8 10 7 10 ...
  .. .. ..@ factors : list()
 $ level2:List of 8
  ..$ specificity          :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:1494549] 0 1 2 3 4 5 6 7 8 11 ...
  .. .. ..@ p       : int [1:150] 0 11070 22299 35820 49231 60945 72757 81515 89851 101568 ...
  .. .. ..@ Dim     : int [1:2] 14240 149
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : Named chr [1:14240] "ACADM" "ACADVL" "ACAT1" "ACVR1" ...
  .. .. .. .. ..- attr(*, "names")= chr [1:14240] "Acadm" "Acadvl" "Acat1" "Acvr1" ...
  .. .. .. ..$ : chr [1:149] "Astro1" "Astro2" "CA1Pyr1" "CA1Pyr2" ...
  .. .. ..@ x       : num [1:1494549] 0.01329 0.01375 0.00448 0.00389 0.09232 ...
  .. .. ..@ factors : list()
  ..$ mean_exp             :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:1494549] 0 1 2 3 4 5 6 7 8 11 ...
  .. .. ..@ p       : int [1:150] 0 11070 22299 35820 49231 60945 72757 81515 89851 101568 ...
  .. .. ..@ Dim     : int [1:2] 14240 149
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : chr [1:14240] "ACADM" "ACADVL" "ACAT1" "ACVR1" ...
  .. .. .. ..$ : chr [1:149] "Astro1" "Astro2" "CA1Pyr1" "CA1Pyr2" ...
  .. .. ..@ x       : num [1:1494549] 1.265 1.544 1.588 0.162 0.103 ...
  .. .. ..@ factors : list()
  ..$ annot                :'data.frame':   149 obs. of  1 variable:
  .. ..$ celltype: chr [1:149] "Astro1" "Astro2" "CA1Pyr1" "CA1Pyr2" ...
  ..$ standardised         : logi TRUE
  ..$ species              :List of 2
  .. ..$ input_species : chr "mouse"
  .. ..$ output_species: chr "human"
  ..$ versions             :List of 3
  .. ..$ EWCE      :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:3] 1 5 5
  .. ..$ orthogene :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:3] 1 3 1
  .. ..$ homologene:Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:6] 1 4 68 19 3 27
  ..$ specificity_quantiles:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:1494549] 0 1 2 3 4 5 6 7 8 11 ...
  .. .. ..@ p       : int [1:150] 0 11070 22299 35820 49231 60945 72757 81515 89851 101568 ...
  .. .. ..@ Dim     : int [1:2] 14240 149
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : Named chr [1:14240] "ACADM" "ACADVL" "ACAT1" "ACVR1" ...
  .. .. .. .. ..- attr(*, "names")= chr [1:14240] "Acadm" "Acadvl" "Acat1" "Acvr1" ...
  .. .. .. ..$ : chr [1:149] "Astro1" "Astro2" "CA1Pyr1" "CA1Pyr2" ...
  .. .. ..@ x       : num [1:1494549] 37 37 28 26 40 11 25 40 23 30 ...
  .. .. ..@ factors : list()
  ..$ specificity_deciles  :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:1494549] 0 1 2 3 4 5 6 7 8 11 ...
  .. .. ..@ p       : int [1:150] 0 11070 22299 35820 49231 60945 72757 81515 89851 101568 ...
  .. .. ..@ Dim     : int [1:2] 14240 149
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : Named chr [1:14240] "ACADM" "ACADVL" "ACAT1" "ACVR1" ...
  .. .. .. .. ..- attr(*, "names")= chr [1:14240] "Acadm" "Acadvl" "Acat1" "Acvr1" ...
  .. .. .. ..$ : chr [1:149] "Astro1" "Astro2" "CA1Pyr1" "CA1Pyr2" ...
  .. .. ..@ x       : num [1:1494549] 10 10 7 7 10 3 7 10 6 8 ...
  .. .. ..@ factors : list()

ctd_quant is the output of prepare_group_quantile() ctd is the QCed ctd loaded from get_ctd()

Example run

 plot_celltype_associations(
+     ctAssocs = ctAssocsTop,
+     ctd = ctd_quant)

TableGrob (1 x 2) "arrange": 2 grobs
  z     cells    name           grob
1 1 (1-1,1-1) arrange gtable[layout]
2 2 (1-1,2-2) arrange gtable[layout]
TableGrob (1 x 2) "arrange": 2 grobs
  z     cells    name           grob
1 1 (1-1,1-1) arrange gtable[layout]
2 2 (1-1,2-2) arrange gtable[layout]
[[1]]
TableGrob (1 x 2) "arrange": 2 grobs
  z     cells    name           grob
1 1 (1-1,1-1) arrange gtable[layout]
2 2 (1-1,2-2) arrange gtable[layout]

[[2]]
TableGrob (1 x 2) "arrange": 2 grobs
  z     cells    name           grob
1 1 (1-1,1-1) arrange gtable[layout]
2 2 (1-1,2-2) arrange gtable[layout]

plot_celltype_associations(
+     ctAssocs = ctAssocsTop,
+     ctd = ctd)
Error in t.default(ctd[[annotLevel]]$specificity_quantiles) :
argument is not a matrix

SessionInfo

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggplot2_3.3.6          data.table_1.14.2      dplyr_1.0.10           MAGMA.Celltyping_2.0.7

loaded via a namespace (and not attached):
  [1] backports_1.4.1               AnnotationHub_3.5.0           BiocFileCache_2.5.0           plyr_1.8.7                    googleAuthR_2.0.0            
  [6] lazyeval_0.2.2                splines_4.2.0                 orthogene_1.3.2               ewceData_1.5.0                BiocParallel_1.31.12         
 [11] GenomeInfoDb_1.33.5           digest_0.6.29                 yulab.utils_0.0.5             htmltools_0.5.3               RNOmni_1.0.1                 
 [16] fansi_1.0.3                   magrittr_2.0.3                memoise_2.0.1                 BSgenome_1.65.2               limma_3.53.6                 
 [21] Biostrings_2.65.3             matrixStats_0.62.0            R.utils_2.12.0                prettyunits_1.1.1             colorspace_2.0-3             
 [26] blob_1.2.3                    rappdirs_0.3.3                gitcreds_0.1.1                crayon_1.5.1                  RCurl_1.98-1.8               
 [31] jsonlite_1.8.0                lme4_1.1-30                   VariantAnnotation_1.43.3      ape_5.6-2                     glue_1.6.2                   
 [36] gtable_0.3.1                  gargle_1.2.0                  zlibbioc_1.43.0               XVector_0.37.1                HGNChelper_0.8.1             
 [41] DelayedArray_0.23.1           car_3.1-0                     SingleCellExperiment_1.19.0   BiocGenerics_0.43.1           abind_1.4-5                  
 [46] scales_1.2.1                  DBI_1.1.3                     rstatix_0.7.0                 Rcpp_1.0.9                    viridisLite_0.4.1            
 [51] xtable_1.8-4                  progress_1.2.2                gridGraphics_0.5-1            tidytree_0.4.0                bit_4.0.4                    
 [56] stats4_4.2.0                  htmlwidgets_1.5.4             httr_1.4.4                    ellipsis_0.3.2                farver_2.1.1                 
 [61] pkgconfig_2.0.3               XML_3.99-0.10                 R.methodsS3_1.8.2             dbplyr_2.2.1                  utf8_1.2.2                   
 [66] labeling_0.4.2                ggplotify_0.1.0               tidyselect_1.1.2              rlang_1.0.5                   reshape2_1.4.4               
 [71] later_1.3.0                   AnnotationDbi_1.59.1          munsell_0.5.0                 BiocVersion_3.16.0            tools_4.2.0                  
 [76] cachem_1.0.6                  cli_3.3.0                     generics_0.1.3                RSQLite_2.2.16                ExperimentHub_2.5.0          
 [81] MungeSumstats_1.5.13          broom_1.0.1                   ggdendro_0.1.23               stringr_1.4.1                 fastmap_1.1.0                
 [86] yaml_2.3.5                    ggtree_3.5.3                  babelgene_22.3                bit64_4.0.5                   fs_1.5.2                     
 [91] purrr_0.3.4                   gh_1.3.0                      KEGGREST_1.37.3               gprofiler2_0.2.1              nlme_3.1-159                 
 [96] mime_0.12                     R.oo_1.25.0                   aplot_0.1.6                   xml2_1.3.3                    biomaRt_2.53.2               
[101] compiler_4.2.0                rstudioapi_0.14               plotly_4.10.0                 filelock_1.0.2                curl_4.3.2                   
[106] png_0.1-7                     interactiveDisplayBase_1.35.0 ggsignif_0.6.3                treeio_1.21.2                 tibble_3.1.8                 
[111] EWCE_1.5.7                    homologene_1.4.68.19.3.27     stringi_1.7.8                 GenomicFeatures_1.49.6        lattice_0.20-45              
[116] Matrix_1.4-1                  nloptr_2.0.3                  vctrs_0.4.1                   pillar_1.8.1                  lifecycle_1.0.1              
[121] BiocManager_1.30.18           bitops_1.0-7                  httpuv_1.6.5                  patchwork_1.1.2               rtracklayer_1.57.0           
[126] GenomicRanges_1.49.1          R6_2.5.1                      BiocIO_1.7.1                  promises_1.2.0.1              gridExtra_2.3                
[131] IRanges_2.31.2                codetools_0.2-18              boot_1.3-28                   MASS_7.3-58.1                 assertthat_0.2.1             
[136] SummarizedExperiment_1.27.2   rjson_0.2.21                  withr_2.5.0                   GenomicAlignments_1.33.1      Rsamtools_2.13.4             
[141] S4Vectors_0.35.3              GenomeInfoDbData_1.2.8        parallel_4.2.0                hms_1.1.2                     grid_4.2.0                   
[146] ggfun_0.0.7                   minqa_1.2.4                   tidyr_1.2.0                   MatrixGenerics_1.9.1          carData_3.0-5                
[151] ggpubr_0.4.0                  piggyback_0.1.3               lubridate_1.8.0               Biobase_2.57.1                shiny_1.7.2                  
[156] restfulr_0.0.15
bschilder commented 1 year ago

Would need a full reprex to understand your particular scenario, but the docs are referring to the fact that celltype_associations_pipeline prepares the quantiles internally.

https://github.com/neurogenomics/MAGMA_Celltyping/blob/7535326f2f5222ac93a3346fc97580c0d5cc2084/R/celltype_associations_pipeline.r#L96