more tests for comp_barplot

tests/testthat/_snaps/comp_barplot.md

@@ -1,3 +1,75 @@
+# comp_barplot doesn't change
+
+    Code
+      levels(p$data$top)
+    Output
+      [1] "other"                               
+      [2] "Allistipes et rel."                  
+      [3] "Clostridium symbiosum et rel."       
+      [4] "Clostridium cellulosi et rel."       
+      [5] "Faecalibacterium prausnitzii et rel."
+      [6] "Prevotella oralis et rel."           
+      [7] "Oscillospira guillermondii et rel."  
+      [8] "Bacteroides vulgatus et rel."        
+      [9] "Prevotella melaninogenica et rel."   
+
+# list of plots generated by group_by works
+
+    Code
+      print(p)
+    Output
+      [1] "overweight"
+    Code
+      levels(plots[[p]]$data$top)
+    Output
+      [1] "other"                               
+      [2] "Allistipes et rel."                  
+      [3] "Clostridium symbiosum et rel."       
+      [4] "Clostridium cellulosi et rel."       
+      [5] "Faecalibacterium prausnitzii et rel."
+      [6] "Prevotella oralis et rel."           
+      [7] "Oscillospira guillermondii et rel."  
+      [8] "Bacteroides vulgatus et rel."        
+      [9] "Prevotella melaninogenica et rel."   
+
+---
+
+    Code
+      print(p)
+    Output
+      [1] "lean"
+    Code
+      levels(plots[[p]]$data$top)
+    Output
+      [1] "other"                               
+      [2] "Allistipes et rel."                  
+      [3] "Clostridium symbiosum et rel."       
+      [4] "Clostridium cellulosi et rel."       
+      [5] "Faecalibacterium prausnitzii et rel."
+      [6] "Prevotella oralis et rel."           
+      [7] "Oscillospira guillermondii et rel."  
+      [8] "Bacteroides vulgatus et rel."        
+      [9] "Prevotella melaninogenica et rel."   
+
+---
+
+    Code
+      print(p)
+    Output
+      [1] "obese"
+    Code
+      levels(plots[[p]]$data$top)
+    Output
+      [1] "other"                               
+      [2] "Allistipes et rel."                  
+      [3] "Clostridium symbiosum et rel."       
+      [4] "Clostridium cellulosi et rel."       
+      [5] "Faecalibacterium prausnitzii et rel."
+      [6] "Prevotella oralis et rel."           
+      [7] "Oscillospira guillermondii et rel."  
+      [8] "Bacteroides vulgatus et rel."        
+      [9] "Prevotella melaninogenica et rel."   
+
 # tt_add_topN_var helper works as expected
 
     Code

tests/testthat/_snaps/comp_barplot/SAMPLE_order-lean.csv

@@ -0,0 +1,39 @@
+"","x"
+"1","Sample-208"
+"2","Sample-212"
+"3","Sample-210"
+"4","Sample-209"
+"5","Sample-207"
+"6","Sample-213"
+"7","Sample-214"
+"8","Sample-38"
+"9","Sample-69"
+"10","Sample-182"
+"11","Sample-61"
+"12","Sample-57"
+"13","Sample-50"
+"14","Sample-58"
+"15","Sample-51"
+"16","Sample-60"
+"17","Sample-52"
+"18","Sample-59"
+"19","Sample-204"
+"20","Sample-181"
+"21","Sample-183"
+"22","Sample-35"
+"23","Sample-34"
+"24","Sample-40"
+"25","Sample-37"
+"26","Sample-33"
+"27","Sample-203"
+"28","Sample-32"
+"29","Sample-71"
+"30","Sample-179"
+"31","Sample-68"
+"32","Sample-36"
+"33","Sample-73"
+"34","Sample-39"
+"35","Sample-180"
+"36","Sample-211"
+"37","Sample-178"
+"38","Sample-56"

tests/testthat/_snaps/comp_barplot/SAMPLE_order-obese.csv

@@ -0,0 +1,39 @@
+"","x"
+"1","Sample-208"
+"2","Sample-212"
+"3","Sample-210"
+"4","Sample-209"
+"5","Sample-207"
+"6","Sample-213"
+"7","Sample-214"
+"8","Sample-38"
+"9","Sample-69"
+"10","Sample-182"
+"11","Sample-61"
+"12","Sample-57"
+"13","Sample-50"
+"14","Sample-58"
+"15","Sample-51"
+"16","Sample-60"
+"17","Sample-52"
+"18","Sample-59"
+"19","Sample-204"
+"20","Sample-181"
+"21","Sample-183"
+"22","Sample-35"
+"23","Sample-34"
+"24","Sample-40"
+"25","Sample-37"
+"26","Sample-33"
+"27","Sample-203"
+"28","Sample-32"
+"29","Sample-71"
+"30","Sample-179"
+"31","Sample-68"
+"32","Sample-36"
+"33","Sample-73"
+"34","Sample-39"
+"35","Sample-180"
+"36","Sample-211"
+"37","Sample-178"
+"38","Sample-56"

tests/testthat/_snaps/comp_barplot/SAMPLE_order-overweight.csv

@@ -0,0 +1,39 @@
+"","x"
+"1","Sample-208"
+"2","Sample-212"
+"3","Sample-210"
+"4","Sample-209"
+"5","Sample-207"
+"6","Sample-213"
+"7","Sample-214"
+"8","Sample-38"
+"9","Sample-69"
+"10","Sample-182"
+"11","Sample-61"
+"12","Sample-57"
+"13","Sample-50"
+"14","Sample-58"
+"15","Sample-51"
+"16","Sample-60"
+"17","Sample-52"
+"18","Sample-59"
+"19","Sample-204"
+"20","Sample-181"
+"21","Sample-183"
+"22","Sample-35"
+"23","Sample-34"
+"24","Sample-40"
+"25","Sample-37"
+"26","Sample-33"
+"27","Sample-203"
+"28","Sample-32"
+"29","Sample-71"
+"30","Sample-179"
+"31","Sample-68"
+"32","Sample-36"
+"33","Sample-73"
+"34","Sample-39"
+"35","Sample-180"
+"36","Sample-211"
+"37","Sample-178"
+"38","Sample-56"

tests/testthat/_snaps/comp_barplot/SAMPLE_order.csv

@@ -0,0 +1,39 @@
+"","x"
+"1","Sample-180"
+"2","Sample-37"
+"3","Sample-36"
+"4","Sample-73"
+"5","Sample-211"
+"6","Sample-178"
+"7","Sample-203"
+"8","Sample-179"
+"9","Sample-71"
+"10","Sample-68"
+"11","Sample-32"
+"12","Sample-33"
+"13","Sample-39"
+"14","Sample-40"
+"15","Sample-34"
+"16","Sample-35"
+"17","Sample-52"
+"18","Sample-56"
+"19","Sample-59"
+"20","Sample-60"
+"21","Sample-57"
+"22","Sample-58"
+"23","Sample-214"
+"24","Sample-51"
+"25","Sample-69"
+"26","Sample-50"
+"27","Sample-61"
+"28","Sample-207"
+"29","Sample-208"
+"30","Sample-213"
+"31","Sample-210"
+"32","Sample-209"
+"33","Sample-212"
+"34","Sample-182"
+"35","Sample-38"
+"36","Sample-183"
+"37","Sample-181"
+"38","Sample-204"

tests/testthat/_snaps/comp_barplot/unique_taxa_order-lean.csv

@@ -0,0 +1,10 @@
+"","x"
+"1","other"
+"2","Allistipes et rel."
+"3","Clostridium symbiosum et rel."
+"4","Clostridium cellulosi et rel."
+"5","Faecalibacterium prausnitzii et rel."
+"6","Prevotella oralis et rel."
+"7","Oscillospira guillermondii et rel."
+"8","Bacteroides vulgatus et rel."
+"9","Prevotella melaninogenica et rel."

tests/testthat/_snaps/comp_barplot/unique_taxa_order-obese.csv

@@ -0,0 +1,10 @@
+"","x"
+"1","other"
+"2","Allistipes et rel."
+"3","Clostridium symbiosum et rel."
+"4","Clostridium cellulosi et rel."
+"5","Faecalibacterium prausnitzii et rel."
+"6","Prevotella oralis et rel."
+"7","Oscillospira guillermondii et rel."
+"8","Bacteroides vulgatus et rel."
+"9","Prevotella melaninogenica et rel."

tests/testthat/_snaps/comp_barplot/unique_taxa_order-overweight.csv

@@ -0,0 +1,10 @@
+"","x"
+"1","other"
+"2","Allistipes et rel."
+"3","Clostridium symbiosum et rel."
+"4","Clostridium cellulosi et rel."
+"5","Faecalibacterium prausnitzii et rel."
+"6","Prevotella oralis et rel."
+"7","Oscillospira guillermondii et rel."
+"8","Bacteroides vulgatus et rel."
+"9","Prevotella melaninogenica et rel."

tests/testthat/_snaps/comp_barplot/unique_taxa_order.csv

@@ -0,0 +1,120 @@
+"","x"
+"1","Gemella"
+"2","Aeromonas"
+"3","Pseudomonas"
+"4","Actinomycetaceae"
+"5","Uncultured Chroococcales"
+"6","Atopobium"
+"7","Staphylococcus"
+"8","Lactobacillus catenaformis et rel."
+"9","Wissella et rel."
+"10","Granulicatella"
+"11","Brachyspira"
+"12","Aquabacterium"
+"13","Leminorella"
+"14","Moraxellaceae"
+"15","Burkholderia"
+"16","Corynebacterium"
+"17","Bacillus"
+"18","Xanthomonadaceae"
+"19","Megamonas hypermegale et rel."
+"20","Eubacterium limosum et rel."
+"21","Propionibacterium"
+"22","Lactococcus"
+"23","Bilophila et rel."
+"24","Oceanospirillum"
+"25","Peptostreptococcus micros et rel."
+"26","Helicobacter"
+"27","Eubacterium cylindroides et rel."
+"28","Yersinia et rel."
+"29","Clostridium ramosum et rel."
+"30","Vibrio"
+"31","Catenibacterium mitsuokai et rel."
+"32","Uncultured Selenomonadaceae"
+"33","Weissella et rel."
+"34","Bulleidia moorei et rel."
+"35","Eubacterium siraeum et rel."
+"36","Uncultured Bacteroidetes"
+"37","Coprobacillus catenaformis et rel."
+"38","Peptococcus niger et rel."
+"39","Eggerthella lenta et rel."
+"40","Campylobacter"
+"41","Lactobacillus salivarius et rel."
+"42","Prevotella ruminicola et rel."
+"43","Desulfovibrio et rel."
+"44","Fusobacteria"
+"45","Haemophilus"
+"46","Proteus et rel."
+"47","Streptococcus intermedius et rel."
+"48","Enterococcus"
+"49","Veillonella"
+"50","Clostridium stercorarium et rel."
+"51","Ruminococcus lactaris et rel."
+"52","Collinsella"
+"53","Lactobacillus gasseri et rel."
+"54","Serratia"
+"55","Alcaligenes faecalis et rel."
+"56","Anaerovorax odorimutans et rel."
+"57","Lactobacillus plantarum et rel."
+"58","Bacteroides intestinalis et rel."
+"59","Roseburia intestinalis et rel."
+"60","Klebisiella pneumoniae et rel."
+"61","Eubacterium ventriosum et rel."
+"62","Eubacterium hallii et rel."
+"63","Clostridium difficile et rel."
+"64","Clostridium (sensu stricto)"
+"65","Oxalobacter formigenes et rel."
+"66","Clostridium colinum et rel."
+"67","Ruminococcus gnavus et rel."
+"68","Eubacterium biforme et rel."
+"69","Megasphaera elsdenii et rel."
+"70","Mitsuokella multiacida et rel."
+"71","Enterobacter aerogenes et rel."
+"72","Papillibacter cinnamivorans et rel."
+"73","Bacteroides stercoris et rel."
+"74","Tannerella et rel."
+"75","Clostridium nexile et rel."
+"76","Ruminococcus bromii et rel."
+"77","Uncultured Clostridiales II"
+"78","Outgrouping clostridium cluster XIVa"
+"79","Eubacterium rectale et rel."
+"80","Streptococcus mitis et rel."
+"81","Lachnobacillus bovis et rel."
+"82","Uncultured Mollicutes"
+"83","Bacteroides plebeius et rel."
+"84","Coprococcus eutactus et rel."
+"85","Bifidobacterium"
+"86","Phascolarctobacterium faecium et rel."
+"87","Anaerostipes caccae et rel."
+"88","Sutterella wadsworthia et rel."
+"89","Lachnospira pectinoschiza et rel."
+"90","Escherichia coli et rel."
+"91","Prevotella tannerae et rel."
+"92","Streptococcus bovis et rel."
+"93","Anaerotruncus colihominis et rel."
+"94","Bacteroides splachnicus et rel."
+"95","Clostridium leptum et rel."
+"96","Dorea formicigenerans et rel."
+"97","Akkermansia"
+"98","Ruminococcus callidus et rel."
+"99","Bacteroides uniformis et rel."
+"100","Clostridium sphenoides et rel."
+"101","Bacteroides ovatus et rel."
+"102","Bryantella formatexigens et rel."
+"103","Parabacteroides distasonis et rel."
+"104","Uncultured Clostridiales I"
+"105","Bacteroides fragilis et rel."
+"106","Butyrivibrio crossotus et rel."
+"107","Dialister"
+"108","Ruminococcus obeum et rel."
+"109","Clostridium orbiscindens et rel."
+"110","Subdoligranulum variable at rel."
+"111","Sporobacter termitidis et rel."
+"112","Allistipes et rel."
+"113","Clostridium symbiosum et rel."
+"114","Clostridium cellulosi et rel."
+"115","Faecalibacterium prausnitzii et rel."
+"116","Prevotella oralis et rel."
+"117","Oscillospira guillermondii et rel."
+"118","Bacteroides vulgatus et rel."
+"119","Prevotella melaninogenica et rel."