plot missing groups or sample columns

[wolvesled]

this issue is replicated with the latest code at ff93a8b

(lefse1.1.2) $ lefse_format_input.py LEfSe.txt input.in -c 1 -o 1000000
(lefse1.1.2) $ lefse_run.py input.in input.res
Number of significantly discriminative features: 11 ( 115 ) before internal wilcoxon
Number of discriminative features with abs LDA score > 2.0 : 11
(lefse1.1.2) $ lefse_plot_res.py input.res input.png
(lefse1.1.2) $ lefse_plot_cladogram.py input.res input.cladogram.png --format png
clade_sep parameter too large, lowered to 0.15016937255859375
(lefse1.1.2) $ lefse_plot_features.py input.in input.res biomarkers_raw_images/
Exporting  Bacteria.Acidobacteria
/home/agean/anaconda3/envs/lefse1.1.2/lib/python3.10/site-packages/lefse/lefse_plot_features.py:99: UserWarning: color is redundantly defined by the 'color' keyword argument and the fmt string "k--" (-> color='k'). The keyword argument will take precedence.
  if params['subcl_median'] == 'y': ax.plot([fr,to-1],[median,median],"k--",linewidth=1,color=params['fore_color'])
Exporting  Bacteria.Acidobacteria.Acidobacteria
Exporting  Bacteria.Proteobacteria.Betaproteobacteria
Exporting  Bacteria.Acidobacteria.Acidobacteria.Subgroup_4
Exporting  Bacteria.Acidobacteria.Acidobacteria.Subgroup_4.Unknown_Family
Exporting  Bacteria.Firmicutes.Clostridia.Clostridiales.Clostridiaceae_1
Exporting  Bacteria.Acidobacteria.Acidobacteria.Subgroup_4.Unknown_Family.Blastocatella
Exporting  Bacteria.Firmicutes.Clostridia.Clostridiales.Clostridiaceae_1.Clostridium_sensu_stricto_1
Exporting  Bacteria.Firmicutes.Clostridia.Clostridiales.Clostridiaceae_1.Clostridium_sensu_stricto_5
Exporting  Bacteria.Proteobacteria.Gammaproteobacteria.Xanthomonadales.Xanthomonadaceae.Lysobacter
Exporting  Bacteria.Proteobacteria.Gammaproteobacteria.Xanthomonadales.Xanthomonadaceae.Thermomonas

and the header of the input.txt:

Class	BS	BS	BS	BS	BS	BS	BS	BS	BS	BS	BS	BS	BS	BS	BS	BS	BS	BS	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	CK	CK	CK	CK	CK	CK	CK	CK	CK	CK	CK	CK	CK	CK	CK	CK	CK	CK	GB	GB	GB	GB	GB	GB	GB	GB	GB	GB	GB	GB	GB	GB	GB	GB	GB	GB	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	S	S	S	S	S	S	S	S	S	S	S	S	S	S	S	S	S
Bacteria	30.6630944407234	28.0821189235188	26.2622912439519	28.464878565641	34.0280283892698	24.8668178701408	22.8306348917591	31.542049846728	23.2917247712663	31.2347608627696	29.4716136471546	33.8675415407855	23.7967782722212	20.9295630477896	16.8389490772952	41.5306788511749	27.9520872441226	41.5160760384886	32.0162510953557	30.5940213210243	34.4588532746106	27.2795123771613	30.7127927313057	30.4716322664274	32.4128984432913	34.3659315147998	34.1582780535325	26.6592442798391	7.51135216952573	27.68968456948	26.8868323548818	27.1602061915718	33.0120737131964	31.2339943342776	27.3729269730603	30.3363761410529	28.8902074636038	28.4102670254606	39.7076572348129	32.3783972938295	29.5300601623964	33.4062458821979	33.1469209633102	35.9502682107585	36.2998335865712	24.3506352716708	23.7893388631373	23.256418251741	28.0696576151122	21.6789806996381	23.8571794215511	36.2356581152507	35.8637953914827	37.3437666915928	32.8514798366666	34.4840999708256	35.1296847853065	72.7115748820974	71.1305790044441	74.8551649646504	43.1020881670534	37.8530510585305	39.7420472592521	39.573396655135	13.5892681862799	40.7100192068216	43.8096802677783	34.1613101198359	25.9357010744197	61.0303454919648	65.8615798885897	64.4623346751006	37.0374356490699	39.2138401788867	33.2591449977964	72.4046368770435	72.6245608431811	74.7023809523809	37.3352244284999	41.5997726788378	44.1844532279315	26.6893642217452	27.5398071316439	32.6823014855592	28.6704100556357	28.2418676698385	21.1531816162314	66.9901899394698	69.2487698195735	60.8118064703387	31.4522599625568	31.8027103021078	24.6580792758741	23.507164544825	26.4721392160309	20.0196976149915	29.3584854263144	29.0867374695461	36.7328458560659	36.2979081847536	29.657192887931	21.7576749491643	25.3858360818968	25.2721021785988	37.7703724904935	44.7464562326465	39.7644054731162
Bacteria|Acidobacteria	0.116097343156955	0.0936070630783959	0.0916965818635867	0.0519394178630046	0.0390953927583303	0.0131863494910069	0.0254684373294524	0.0666400106624017	0.0748273868235774	0.112535167239762	0.0768726401229962	0.0849697885196375	0.206899949096044	0.13274902437464	0.115959314846105	0.0550750652741514	0.0774708739310509	0.058671673316123	0.220398842242226	0.175843499285636	0.280020661718729	0.0787826014844301	0.0575864863711982	0.0598265031408914	0.240919199406968	0.340975043528729	0.243540381314654	0.181772738633523	0.0567608476286579	0.381926683716965	0.504170402828768	0.372775722981041	0.431582291887312	0.0634560906515581	0.128162407402661	0.112542203326247	0.233105172815699	0.0672738563444421	0.301729918197667	0.08865041409075	0.132525558500568	0.0658848333113717	0.265071925004041	0.308317040156414	0.465475242987724	0.28402931355969	0.143327640888021	0.223469493815612	0.346141461843941	0.282720144752714	0.258510366009726	0.208843625112801	0.0965134515623115	0.0293772032902468	0.05066913057733	0.0486239424292522	0.0620501365103003	0.024137546882543	0.00850539029109698	0.0196386488609584	0.0603248259860789	0.0473225404732254	0.0794070937003706	0.0941638861026386	0.0581670120333006	0.160408619852677	0.112943302462164	0.0952873154817662	0.0768927035058916	0.0262731532162718	0.0308331106497564	0.0123223527478847	0.0627813951819764	0.0294221489937625	0.143234905244601	0.00990785693054592	0.00598850207601405	0.00220458553791887	0.0389343122531843	0.0449906466813478	0.0395256916996047	0.159129598105248	0.156985871271586	0.17595455345248	0.293632804450855	0.154901526886479	0.182652910105149	0.0438321853475266	0.0262438490978677	0.0379557480631405	0.130382455201926	0.103591890234879	0.172410934831982	0.0665849890800618	0.0615222358938302	0.0851788756388416	0.146417869790248	0.0898833881306621	0.162995494985625	0.0795544948289578	0.148168103448276	0.175238473110814	0.161802227892215	0.288579724602312	0.122664267898761	0.0730673681134006	0.0674503757949509
Bacteria|Actinobacteria	0.82830989060058	1.02329539410701	1.00085843608553	1.69322502233395	1.21496451341273	2.93264412679994	2.139348735674	1.25283220045315	1.65980748954117	0.803376055017193	1.14404576183047	1.13765105740181	0.821031544031922	0.799692917919519	0.977371367988603	1.56453981723238	1.38553678376687	1.50903543769068	1.30114979155049	1.79415320364875	1.21795394611641	4.48646183190281	2.86652732158853	2.84923721208495	1.48026315789474	1.69762042948346	1.5470612793988	1.80409443093772	0.113521695257316	2.13128729752771	0.795168084998393	0.765937618312607	0.680470239356069	1.88101983002833	2.46584471842719	2.32274602976116	0.436542414545763	0.507141378596564	1.0694649322784	4.05458999183483	3.22058142959317	3.50243773883252	1.20575400032326	1.43630621146037	1.2468948218894	1.22284376219592	1.69553549646255	1.58767279908533	1.0759901255769	1.34574788902292	1.27975428717686	1.08031455459585	1.57739172397153	2.28340989210554	1.16240946618581	0.717203150831469	1.38682055100521	0.271083218834713	0.433774904845946	0.375589159465829	1.42227378190255	1.27272727272727	1.7204870301747	1.40427012753065	0.737993965172502	1.01943899195846	1.10479084953899	0.702542071772344	0.442652590452836	0.823225467443184	0.628995457255031	0.751663517620965	0.89867082817629	1.23278804283865	1.01366240634641	0.34083027841078	0.461114659853082	0.440917107583774	1.07625563157017	1.00636972839857	1.45718050065876	2.30182814003405	1.70441803094864	1.45790915717769	1.79785699567278	0.146603230803275	1.37730167349558	0.540596952619495	0.376161837069437	0.875214896514769	0.775608451457609	0.471448806579142	0.606753866812553	2.35977201299739	2.55097556688346	1.03545570698467	1.00789975483519	1.39319251602526	0.830824259162837	0.807244138705602	0.737473060344828	0.704260278728364	0.847905905781318	0.575378092879919	1.3758842049311	1.12036631107214	1.75370977066872

the output res and cladogram only show 4 groups:

the feature plot is ok.

[wolvesled]

sorry, it's a mistake