diff --git a/Project.toml b/Project.toml index d3eee42..0a10e77 100644 --- a/Project.toml +++ b/Project.toml @@ -4,6 +4,7 @@ authors = ["Aadam "] 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" diff --git a/notebooks/00-pdac_nac.ipynb b/notebooks/00-pdac_nac.ipynb index f685d4e..0002d29 100644 --- a/notebooks/00-pdac_nac.ipynb +++ b/notebooks/00-pdac_nac.ipynb @@ -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", @@ -45,7 +46,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 4, "metadata": {}, "outputs": [ { @@ -66,7 +67,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ @@ -85,7 +86,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -100,7 +101,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 7, "metadata": {}, "outputs": [ { @@ -109,7 +110,7 @@ "\"neoadjuvant_chemo\"" ] }, - "execution_count": 14, + "execution_count": 7, "metadata": {}, "output_type": "execute_result" } @@ -130,7 +131,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 8, "metadata": {}, "outputs": [ { @@ -139,22 +140,10 @@ "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" ] }, @@ -162,9 +151,9 @@ "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" ] }, { @@ -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" ] } ], @@ -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,