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fix: add CSV dep
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@aadimator
aadimator committed Jul 31, 2024
1 parent 3860a17 commit 7d4a744
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Showing 2 changed files with 74 additions and 28 deletions.
1 change: 1 addition & 0 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ authors = ["Aadam <[email protected]>"]
version = "1.0.0-DEV"

[deps]
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
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101 changes: 73 additions & 28 deletions notebooks/00-pdac_nac.ipynb
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Expand Up @@ -2,10 +2,11 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"using CSV\n",
"using Muon\n",
"using RData\n",
"using Revise\n",
Expand Down Expand Up @@ -45,7 +46,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"outputs": [
{
Expand All @@ -66,7 +67,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -85,7 +86,7 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -100,7 +101,7 @@
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 7,
"metadata": {},
"outputs": [
{
Expand All @@ -109,7 +110,7 @@
"\"neoadjuvant_chemo\""
]
},
"execution_count": 14,
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -130,7 +131,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 8,
"metadata": {},
"outputs": [
{
Expand All @@ -139,32 +140,20 @@
"text": [
"Running for CC10\n",
"Running for Yes\n",
"Updated\n",
"Preparing L-R presence/absence matrix\n",
"Calculating L-R pairs correlation\n",
"Preparing for cooccurrence\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Preparing for cooccurrence\n",
"Cooccurrence calculation starts...\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\u001b[32mCalculate Incidence 100%|████████████████████████████████| Time: 0:02:17\u001b[39mm\n",
"\u001b[32mCalculate Co-occurrences 100%|███████████████████████████| Time: 0:02:15\u001b[39m\n",
"\u001b[32mMain Comp 100%|██████████████████████████████████████████| Time: 0:00:43\u001b[39m\n"
"\u001b[32mCalculate Incidence 100%|████████████████████████████████| Time: 0:01:04\u001b[39m\n",
"\u001b[32mCalculate Co-occurrences 100%|███████████████████████████| Time: 0:01:17\u001b[39m\n",
"\u001b[32mMain Comp 100%|██████████████████████████████████████████| Time: 0:00:59\u001b[39m\n"
]
},
{
Expand Down Expand Up @@ -192,7 +181,63 @@
"name": "stderr",
"output_type": "stream",
"text": [
"\u001b[32mCalculate Significantly occurring pairs 2%|█ | ETA: 1 days, 7:24:31\u001b[39mm\r"
"\u001b[32mCalculate Significantly occurring pairs 1%|▏ | ETA: 16:43:51\u001b[39m"
]
},
{
"ename": "LoadError",
"evalue": "InterruptException:",
"output_type": "error",
"traceback": [
"InterruptException:",
"",
"Stacktrace:",
" [1] Array",
" @ ./boot.jl:448 [inlined]",
" [2] Array",
" @ ./boot.jl:467 [inlined]",
" [3] _getindex_array(idx::Muon.Index{String, UInt32}, elem::String)",
" @ Muon ~/.julia/packages/Muon/OxkVO/src/index.jl:78",
" [4] getindex(idx::Muon.Index{String, UInt32}, elem::String, #unused#::Val{true})",
" @ Muon ~/.julia/packages/Muon/OxkVO/src/index.jl:181",
" [5] #5",
" @ ./array.jl:0 [inlined]",
" [6] MappingRF",
" @ ./reduce.jl:93 [inlined]",
" [7] _foldl_impl(op::Base.MappingRF{Muon.var\"#5#6\"{Muon.Index{String, UInt32}, Val{true}}, Base.BottomRF{typeof(vcat)}}, init::Base._InitialValue, itr::Vector{String})",
" @ Base ./reduce.jl:62",
" [8] foldl_impl",
" @ ./reduce.jl:48 [inlined]",
" [9] mapfoldl_impl",
" @ ./reduce.jl:44 [inlined]",
" [10] #mapfoldl#214",
" @ ./reduce.jl:160 [inlined]",
" [11] mapfoldl",
" @ ./reduce.jl:160 [inlined]",
" [12] #mapreduce#218",
" @ ./reduce.jl:287 [inlined]",
" [13] mapreduce",
" @ ./reduce.jl:287 [inlined]",
" [14] #reduce#220",
" @ ./reduce.jl:456 [inlined]",
" [15] reduce",
" @ ./reduce.jl:456 [inlined]",
" [16] getindex(idx::Muon.Index{String, UInt32}, elems::Vector{String}, x::Val{true})",
" @ Muon ~/.julia/packages/Muon/OxkVO/src/index.jl:174",
" [17] getindex(idx::Muon.Index{String, UInt32}, elems::Vector{String}, x::Bool)",
" @ Muon ~/.julia/packages/Muon/OxkVO/src/index.jl:168",
" [18] convertidx",
" @ ~/.julia/packages/Muon/OxkVO/src/util.jl:88 [inlined]",
" [19] getindex(adata::AnnData, I::Vector{String}, J::String)",
" @ Muon ~/.julia/packages/Muon/OxkVO/src/anndata.jl:267",
" [20] macro expansion",
" @ /N/project/aadam/workspace/ISCHIA.jl/src/lr_enrichment.jl:83 [inlined]",
" [21] macro expansion",
" @ ~/.julia/packages/ProgressMeter/kVZZH/src/ProgressMeter.jl:1008 [inlined]",
" [22] find_enriched_LR_pairs(adata::AnnData, COI::Vector{String}, Condition::Vector{String}, LR_list::Vector{String}, LR_pairs::Vector{String}, exp_th::Int64, corr_th::Float64; cc_column::String, condition_column::String)",
" @ ISCHIA /N/project/aadam/workspace/ISCHIA.jl/src/lr_enrichment.jl:74",
" [23] top-level scope",
" @ ./In[8]:5"
]
}
],
Expand Down Expand Up @@ -222,15 +267,15 @@
],
"metadata": {
"kernelspec": {
"display_name": "Julia 1.9.3",
"display_name": "Julia 1.6.3",
"language": "julia",
"name": "julia-1.9"
"name": "julia-1.6"
},
"language_info": {
"file_extension": ".jl",
"mimetype": "application/julia",
"name": "julia",
"version": "1.10.4"
"version": "1.6.3"
}
},
"nbformat": 4,
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