require 'nyaplot'
require 'bionya'

true

path = File.expand_path("../data/operon.csv", __FILE__)
df_operon = Nyaplot::DataFrame.from_csv(path)

	genename	geneannotation	operonname	operoncomments	probeset	locbegin	locend
1	thrA	aspartokinase I/homoserine dehydrogenase I	thr	threonine biosynthesis	thrA_b0002_st	337	2799
2	thrB	homoserine kinase	thr	threonine biosynthesis	thrB_b0003_st	2801	3733
3	thrC	threonine synthase	thr	threonine biosynthesis	thrC_b0004_st	3734	5020
4	dnaK	DNA biosynthesis; heat shock protein	dnaK	DNA biosynthesis	dnaK_b0014_st	12163	14079
5	dnaJ	DNA biosynthesis; heat shock protein	dnaK	DNA biosynthesis	dnaJ_b0015_st	14168	15298
6	yaaC	35K hypothetical	ileS-lsp	tRNA synthetase & peptidase	ribF_b0025_st	21407	22348
7	ileS	isoleucine tRNA synthetase (EC 6.1.1.5)	ileS-lsp	tRNA synthetase & peptidase	ileS_b0026_st	22391	25206
8	lspA	prolipoprotein signal peptidase (SPaseII) (EC 3.4 99 35)	ileS-lsp	tRNA synthetase & peptidase	lspA_b0027_st	25208	25701
9	carA	carbamoyl-phosphate synthetase subunit A	carAB	carbamoyl-phosphate synthetase	carA_b0032_st	29651	30799
10	carB	carbamoyl-phosphate synthetase subunit B	carAB	carbamoyl-phosphate synthetase	carB_b0033_st	30817	34038
11	caiT	probable carnitine transporter	cai	probable carnitine operon	caiT_b0040_st	40417	41931
12	caiA	probable carnitine operon oxidoreductase CaiA	cai	probable carnitine operon	caiA_b0039_st	39244	40386
13	caiB	L-carnitine dehydratase	cai	probable carnitine operon	caiB_b0038_st	37898	39115
14	caiC	probable crotonobetaine/carnitine-CoA ligase	cai	probable carnitine operon	caiC_b0037_st	36271	37839
15	caiD	carnitine racemase	cai	probable carnitine operon	caiD_b0036_st	35393	36270
16	caiE	carnitine operon protein CaiE	cai	probable carnitine operon	caiE_b0035_st	34781	35376
...	...	...	...	...	...	...	...
548	creD	inner membrane protein CreD	creABCD	phosphate sensor	creD_b4400_st	4635747	4637099

begin_arr = [0]; end_arr=[336]; size_arr=[337]; if_operon_arr=["no"]; name_arr = [SecureRandom.uuid ]; df_arr = []
df_operon.filter! {|row| !(row[:locbegin].is_a?(String) || row[:locend].is_a?(String))}

df_operon.column(:operonname).to_a.uniq.each do |name|
  df_part = df_operon.filter{|row| row[:operonname].to_s == name.to_s}
  operon_begin = df_part.column(:locbegin).to_a.min
  operon_end = df_part.locend.to_a.max
  
  prev_end = end_arr.clone.pop
  if operon_begin - prev_end > 1
    name_arr.push(SecureRandom.uuid)
    begin_arr.push(prev_end+1)
    end_arr.push(operon_begin-1)
    size_arr.push(operon_begin - prev_end -1)
    if_operon_arr.push("no")
  end
  
  name_arr.push(name)
  begin_arr.push(operon_begin)
  end_arr.push(operon_end)
  size_arr.push(operon_end - operon_begin + 1)
  if_operon_arr.push("yes")
end
df_operon_info = Nyaplot::DataFrame.new({name: name_arr, begin: begin_arr, end: end_arr, size: size_arr, if_operon: if_operon_arr})
df_operon_info

name	begin	end	size	if_operon
e17eaf65-8992-477d-afb3-68529cab2c82	0	336	337	no
thr	337	5020	4684	yes
2095ab6d-0e82-4d9c-b643-b3f4bdf4cc23	5021	12162	7142	no
dnaK	12163	15298	3136	yes
398c2464-338d-4fbd-b9ee-95b600f592c8	15299	21406	6108	no
ileS-lsp	21407	25701	4295	yes
7d9bb493-9b36-4158-aace-15af8ca30370	25702	29650	3949	no
carAB	29651	34038	4388	yes
5a6f8966-32de-46e1-bf6a-9f81cf85e3d3	34039	34780	742	no
cai	34781	41931	7151	yes
121e64d2-6da7-4284-89cd-1db9d2fb5904	41932	42366	435	no
fix	42367	45462	3096	yes
0c0a594e-1d60-46b1-b49e-e540d3e398f2	45463	50379	4917	no
surA-pdxA-ksgA-apaGH	50380	54702	4323	yes
505b5b25-b3d3-4f10-9eef-c34ebe2122e1	54703	65854	11152	no
araBAD	65855	70048	4194	yes
...	...	...	...	...
creABCD	4633090	4637099	4010	yes

df_arr = []
df_operon_info.each_row do |row|
  axis_arr=[]
  row[:begin].step(row[:end], 1000){|val| axis_arr.push(val)}
  val_arr=Array.new(axis_arr.length, -0)
  name_arr=Array.new(axis_arr.length, '')
  df_arr.push(Nyaplot::DataFrame.new({axis: axis_arr, val: val_arr, name: name_arr}))
end
df_operon_info.df = df_arr
df_operon_info

name	begin	end	size	if_operon	df
e17eaf65-8992-477d-afb3-68529cab2c82	0	336	337	no	axis val name 0 0
thr	337	5020	4684	yes	axis val name 337 0 1337 0 2337 0 3337 0 4337 0
2095ab6d-0e82-4d9c-b643-b3f4bdf4cc23	5021	12162	7142	no	axis val name 5021 0 6021 0 7021 0 8021 0 9021 0 10021 0 11021 0 12021 0
dnaK	12163	15298	3136	yes	axis val name 12163 0 13163 0 14163 0 15163 0
398c2464-338d-4fbd-b9ee-95b600f592c8	15299	21406	6108	no	axis val name 15299 0 16299 0 17299 0 18299 0 19299 0 20299 0 21299 0
ileS-lsp	21407	25701	4295	yes	axis val name 21407 0 22407 0 23407 0 24407 0 25407 0
7d9bb493-9b36-4158-aace-15af8ca30370	25702	29650	3949	no	axis val name 25702 0 26702 0 27702 0 28702 0
carAB	29651	34038	4388	yes	axis val name 29651 0 30651 0 31651 0 32651 0 33651 0
5a6f8966-32de-46e1-bf6a-9f81cf85e3d3	34039	34780	742	no	axis val name 34039 0
cai	34781	41931	7151	yes	axis val name 34781 0 35781 0 36781 0 37781 0 38781 0 39781 0 40781 0 41781 0
121e64d2-6da7-4284-89cd-1db9d2fb5904	41932	42366	435	no	axis val name 41932 0
fix	42367	45462	3096	yes	axis val name 42367 0 43367 0 44367 0 45367 0
0c0a594e-1d60-46b1-b49e-e540d3e398f2	45463	50379	4917	no	axis val name 45463 0 46463 0 47463 0 48463 0 49463 0
surA-pdxA-ksgA-apaGH	50380	54702	4323	yes	axis val name 50380 0 51380 0 52380 0 53380 0 54380 0
505b5b25-b3d3-4f10-9eef-c34ebe2122e1	54703	65854	11152	no	axis val name 54703 0 55703 0 56703 0 57703 0 58703 0 59703 0 60703 0 61703 0 62703 0 63703 0 64703 0 65703 0
araBAD	65855	70048	4194	yes	axis val name 65855 0 66855 0 67855 0 68855 0 69855 0
...	...	...	...	...	...
creABCD	4633090	4637099	4010	yes	axis val name 4633090 0 4634090 0 4635090 0 4636090 0 4637090 0

path = File.expand_path("../data/ttest.csv", __FILE__)
df_ttest = Nyaplot::DataFrame.from_csv(path)

name	statistic	dm	pvalue
aceA_b4015_st	-2.66477534128427	-0.231420053466338	0.0372855953591475
alpA_b2624_st	-2.59430119116714	-0.314091063837314	0.040974544243199
amn_b1982_st	2.50075233999086	0.300768027982889	0.0464808997782366
ampE_b0111_st	3.22741963510934	0.491886566026404	0.0179686874331823
aroA_b0908_st	-2.6281727788343	-0.677562777505308	0.0391552776749673
arp_b4017_st	-3.09780159566518	-0.203635693987595	0.0211758093340619
artI_b0863_st	3.91803669738052	1.11440735214105	0.00781965224654806
artP_b0864_st	3.03766268937103	0.767133218653141	0.0228714672660835
asd_b3433_st	2.85224988311835	0.371215322942883	0.0290956715334605
aspC_b0928_st	-3.73505182820475	-0.557002362309087	0.00967879356954946
atpB_b3738_st	-4.47240462758734	-0.644712240554911	0.00422655258946847
atpD_b3732_st	-2.58770662044562	-0.694185677478369	0.0413390790459209
atpF_b3736_st	-2.57794520925451	-0.478497937246775	0.0418850057120005
atpG_b3733_st	-5.94520060825289	-0.598274871270332	0.00101205103480581
atpI_b3739_st	-2.6778774179882	-0.604098316763061	0.0366396699210827
b0836_st	2.51445251943079	1.23976163226646	0.0456278087140453
...	...	...	...
ytfK_b4217_st	7.81549357554911	2.64137844388281	0.000231537137148067

df_operon

	genename	geneannotation	operonname	operoncomments	probeset	locbegin	locend
1	thrA	aspartokinase I/homoserine dehydrogenase I	thr	threonine biosynthesis	thrA_b0002_st	337	2799
2	thrB	homoserine kinase	thr	threonine biosynthesis	thrB_b0003_st	2801	3733
3	thrC	threonine synthase	thr	threonine biosynthesis	thrC_b0004_st	3734	5020
4	dnaK	DNA biosynthesis; heat shock protein	dnaK	DNA biosynthesis	dnaK_b0014_st	12163	14079
5	dnaJ	DNA biosynthesis; heat shock protein	dnaK	DNA biosynthesis	dnaJ_b0015_st	14168	15298
6	yaaC	35K hypothetical	ileS-lsp	tRNA synthetase & peptidase	ribF_b0025_st	21407	22348
7	ileS	isoleucine tRNA synthetase (EC 6.1.1.5)	ileS-lsp	tRNA synthetase & peptidase	ileS_b0026_st	22391	25206
8	lspA	prolipoprotein signal peptidase (SPaseII) (EC 3.4 99 35)	ileS-lsp	tRNA synthetase & peptidase	lspA_b0027_st	25208	25701
9	carA	carbamoyl-phosphate synthetase subunit A	carAB	carbamoyl-phosphate synthetase	carA_b0032_st	29651	30799
10	carB	carbamoyl-phosphate synthetase subunit B	carAB	carbamoyl-phosphate synthetase	carB_b0033_st	30817	34038
11	caiT	probable carnitine transporter	cai	probable carnitine operon	caiT_b0040_st	40417	41931
12	caiA	probable carnitine operon oxidoreductase CaiA	cai	probable carnitine operon	caiA_b0039_st	39244	40386
13	caiB	L-carnitine dehydratase	cai	probable carnitine operon	caiB_b0038_st	37898	39115
14	caiC	probable crotonobetaine/carnitine-CoA ligase	cai	probable carnitine operon	caiC_b0037_st	36271	37839
15	caiD	carnitine racemase	cai	probable carnitine operon	caiD_b0036_st	35393	36270
16	caiE	carnitine operon protein CaiE	cai	probable carnitine operon	caiE_b0035_st	34781	35376
...	...	...	...	...	...	...	...
548	creD	inner membrane protein CreD	creABCD	phosphate sensor	creD_b4400_st	4635747	4637099

df_operon.filter{|row| row[:probeset] == "aceA_b4015_st"}.column(:locbegin).to_a[0]

4214688

df_ttest.each_row do |row1|
  name = row1[:name]
  locbegin = df_operon.filter{|row| row[:probeset] == name}.column(:locbegin).to_a[0]
  next if locbegin.nil?
  df_operon_info.each_row do |row|
    if locbegin > row[:begin] && locbegin < row[:end]
      row[:df].each_row do |nest_row|
        if locbegin < nest_row[:axis] + 1000 && locbegin > nest_row[:axis]
          nest_row[:val] = row1[:dm]
          nest_row[:name] = row1[:name]
        end
      end
    end
  end
end
df_operon_info

name	begin	end	size	if_operon	df
e17eaf65-8992-477d-afb3-68529cab2c82	0	336	337	no	axis val name 0 0
thr	337	5020	4684	yes	axis val name 337 0 1337 0 2337 0 3337 0 4337 0
2095ab6d-0e82-4d9c-b643-b3f4bdf4cc23	5021	12162	7142	no	axis val name 5021 0 6021 0 7021 0 8021 0 9021 0 10021 0 11021 0 12021 0
dnaK	12163	15298	3136	yes	axis val name 12163 0 13163 0 14163 0 15163 0
398c2464-338d-4fbd-b9ee-95b600f592c8	15299	21406	6108	no	axis val name 15299 0 16299 0 17299 0 18299 0 19299 0 20299 0 21299 0
ileS-lsp	21407	25701	4295	yes	axis val name 21407 0 22407 0 23407 0 24407 0 25407 0
7d9bb493-9b36-4158-aace-15af8ca30370	25702	29650	3949	no	axis val name 25702 0 26702 0 27702 0 28702 0
carAB	29651	34038	4388	yes	axis val name 29651 0 30651 0 31651 0 32651 0 33651 0
5a6f8966-32de-46e1-bf6a-9f81cf85e3d3	34039	34780	742	no	axis val name 34039 0
cai	34781	41931	7151	yes	axis val name 34781 0 35781 0 36781 0 37781 0 38781 0 39781 0 40781 0 41781 0
121e64d2-6da7-4284-89cd-1db9d2fb5904	41932	42366	435	no	axis val name 41932 0
fix	42367	45462	3096	yes	axis val name 42367 0 43367 0 44367 0 45367 0
0c0a594e-1d60-46b1-b49e-e540d3e398f2	45463	50379	4917	no	axis val name 45463 0 46463 0 47463 0 48463 0 49463 0
surA-pdxA-ksgA-apaGH	50380	54702	4323	yes	axis val name 50380 0 51380 0 52380 0 53380 0 54380 0
505b5b25-b3d3-4f10-9eef-c34ebe2122e1	54703	65854	11152	no	axis val name 54703 0 55703 0 56703 0 57703 0 58703 0 59703 0 60703 0 61703 0 62703 0 63703 0 64703 0 65703 0
araBAD	65855	70048	4194	yes	axis val name 65855 0 66855 0 67855 0 68855 0 69855 0
...	...	...	...	...	...
creABCD	4633090	4637099	4010	yes	axis val name 4633090 0 4634090 0 4635090 0 4636090 0 4637090 0

df_operon_info.each_row do |row|
  unless row[:df].val.to_a.all?{|val| !val.nil?}
    print "hoge"
  end
end
""

""

plot = Nyaplot::CircularPlot.new(df_operon_info, :name, :df)
plot.color(['#999999','#ef8a62'])
plot.fill_by(:if_operon)
arc = plot.add(1, :arc, :axis, :val)
arc.color(["#a50026"])
labels = plot.add(2, :labels, :axis, :name)
labels.text_size(0.5)
plot.text_size("0")
plot.padding(0.2)
plot.show

plot.group_by

:name