david-barnett/microViz
Microbiome Data Analysis and Visualization

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tests/testthat/_snaps/ord_explore.md

tests/testthat/_snaps/ord_explore.md
In david-barnett/microViz: Microbiome Data Analysis and Visualization

ord_explore_init stays the same

Code
  ord_explore_init(dietswap)
Output
  $data
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 130 taxa and 222 samples ]
  sample_data() Sample Data:       [ 222 samples by 9 sample variables ]
  tax_table()   Taxonomy Table:    [ 130 taxa by 4 taxonomic ranks ]

  psExtra info:
  tax_agg = "unique" tax_trans = "identity"

  $info
  $info$rank
  [1] "unique"

  $info$trans
  [1] "identity"

  $info$scale
  character(0)

  $info$dist
  [1] "none"

  $info$ord
  [1] "auto"

  $info$constraints
  NULL

  $info$conditions
  NULL

  $info$isCon
  [1] FALSE


  $vars
  $vars$all
  [1] "subject"                "sex"                    "nationality"           
  [4] "group"                  "sample"                 "timepoint"             
  [7] "timepoint.within.group" "bmi_group"              "SAMPLE"

  $vars$num
  [1] "timepoint"              "timepoint.within.group"

  $vars$cat
  [1] "subject"     "sex"         "nationality" "group"       "sample"     
  [6] "bmi_group"   "SAMPLE"

  $vars$shapeSafe
  [1] "sex"                    "nationality"            "group"                 
  [4] "timepoint.within.group" "bmi_group"


  $ranks
  [1] "Phylum" "Family" "Genus"  "unique"

  $warn
  [1] FALSE

Code
  ord_explore_init(ord)
Output
  $data
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 130 taxa and 222 samples ]
  sample_data() Sample Data:       [ 222 samples by 11 sample variables ]
  tax_table()   Taxonomy Table:    [ 130 taxa by 4 taxonomic ranks ]

  otu_get(counts = TRUE)         [ 130 taxa and 222 samples ]

  psExtra info:
  tax_agg = "Genus" tax_trans = "clr"

  ordination of class: rda cca 
  rda(formula = OTU ~ weight + female, data = data)
  Ordination info:
  method = 'RDA'    constraints = 'weight+female'

  $info
  $info$rank
  [1] "Genus"

  $info$trans
  [1] "clr"

  $info$scale
  character(0)

  $info$dist
  [1] "none"

  $info$ord
  [1] "RDA"

  $info$constraints
  [1] "weight" "female"

  $info$conditions
  NULL

  $info$isCon
  [1] TRUE


  $vars
  $vars$all
   [1] "subject"                "sex"                    "nationality"           
   [4] "group"                  "sample"                 "timepoint"             
   [7] "timepoint.within.group" "bmi_group"              "weight"                
  [10] "female"                 "SAMPLE"

  $vars$num
  [1] "timepoint"              "timepoint.within.group" "weight"                
  [4] "female"

  $vars$cat
  [1] "subject"     "sex"         "nationality" "group"       "sample"     
  [6] "bmi_group"   "SAMPLE"

  $vars$shapeSafe
  [1] "sex"                    "nationality"            "group"                 
  [4] "timepoint.within.group" "bmi_group"              "weight"                
  [7] "female"


  $ranks
  [1] "Phylum" "Family" "Genus"  "unique"

  $warn
  [1] FALSE

Code
  ord_explore_init(esophagus)
Message
  Note: Replacing missing sample_data with a dataframe of only sample_names.
  Try `ps <- phyloseq_validate(ps, verbose = FALSE)` to avoid this message
  Note: Replacing missing tax_table with a 1-column table of only taxa_names.
  Try `ps <- phyloseq_validate(ps, verbose = FALSE)` to avoid this message
Output
  $data
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 58 taxa and 3 samples ]
  sample_data() Sample Data:       [ 3 samples by 1 sample variables ]
  tax_table()   Taxonomy Table:    [ 58 taxa by 1 taxonomic ranks ]
  phy_tree()    Phylogenetic Tree: [ 58 tips and 57 internal nodes ]

  psExtra info:
  tax_agg = "unique" tax_trans = "identity"

  $info
  $info$rank
  [1] "unique"

  $info$trans
  [1] "identity"

  $info$scale
  character(0)

  $info$dist
  [1] "none"

  $info$ord
  [1] "auto"

  $info$constraints
  NULL

  $info$conditions
  NULL

  $info$isCon
  [1] FALSE


  $vars
  $vars$all
  [1] "SAMPLE"

  $vars$num
  character(0)

  $vars$cat
  NULL

  $vars$shapeSafe
  NULL


  $ranks
  [1] "unique"

  $warn
  [1] FALSE

dist_choices helper works

Code
  dist_choices(dietswap, type = "tree")
Output
  named character(0)

Code
  dist_choices(esophagus, type = "tree")
Output
  gunifrac: Generalised UniFrac, alpha=0.5 
                                "gunifrac" 
                wunifrac: weighted UniFrac 
                                "wunifrac" 
               unifrac: unweighted UniFrac 
                                 "unifrac" 
                                      <NA> 
                                        NA 
                                     dpcoa 
                                   "dpcoa"

ord_choices helper works

Code
  cat(type)
Output
  all
Code
  cat(ord_choices(type))
Output
  auto PCA PCoA RDA CAP CCA NMDS

Code
  cat(type)
Output
  constrained
Code
  cat(ord_choices(type))
Output
  auto RDA CAP CCA

Code
  cat(type)
Output
  unconstrained
Code
  cat(ord_choices(type))
Output
  auto PCA PCoA NMDS

Code
  cat(type)
Output
  dist
Code
  cat(ord_choices(type))
Output
  auto PCoA CAP NMDS

Code
  cat(type)
Output
  noDist
Code
  cat(ord_choices(type))
Output
  auto PCA RDA CCA

Code
  cat(type)
Output
  constrained dist
Code
  cat(ord_choices(type))
Output
  auto CAP

Code
  cat(type)
Output
  unconstrained dist
Code
  cat(ord_choices(type))
Output
  auto PCoA NMDS

Code
  cat(type)
Output
  constrained noDist
Code
  cat(ord_choices(type))
Output
  auto RDA CCA

Code
  cat(type)
Output
  unconstrained noDist
Code
  cat(ord_choices(type))
Output
  auto PCA

ord_code helper works

Code
  for (x in list(p, a, c)) cat(x, "\t")
Output
  FALSE     0.5         
Code
  ord_code(rank = "Genus", trans = "identity", dist = "none", ord = "RDA", const = c,
    conds = NULL, x = 1, y = 2, colour = "v", fill = "v", shape = "var", alpha = a,
    size = 1, plot_taxa = p, ellipses = FALSE, chulls = FALSE, paths = NULL)
Output
  your_phyloseq %>%
   tax_transform(rank = "Genus", trans = "identity") %>%
   ord_calc(
    method = "RDA"
   ) %>% 
   ord_plot(
    axes = c(1, 2),
    colour = "v", fill = "v",
    shape = "var", alpha = 0.5,
    size = 1
   )

Code
  for (x in list(p, a, c)) cat(x, "\t")
Output
  FALSE     0.5     test1 test2     
Code
  ord_code(rank = "Genus", trans = "identity", dist = "none", ord = "RDA", const = c,
    conds = NULL, x = 1, y = 2, colour = "v", fill = "v", shape = "var", alpha = a,
    size = 1, plot_taxa = p, ellipses = FALSE, chulls = FALSE, paths = NULL)
Output
  your_phyloseq %>%
   tax_transform(rank = "Genus", trans = "identity") %>%
   ord_calc(
    constraints = c("test1", "test2"),
    method = "RDA"
   ) %>% 
   ord_plot(
    axes = c(1, 2),
    colour = "v", fill = "v",
    shape = "var", alpha = 0.5,
    size = 1
   )

Code
  for (x in list(p, a, c)) cat(x, "\t")
Output
  FALSE     aVariable       
Code
  ord_code(rank = "Genus", trans = "identity", dist = "none", ord = "RDA", const = c,
    conds = NULL, x = 1, y = 2, colour = "v", fill = "v", shape = "var", alpha = a,
    size = 1, plot_taxa = p, ellipses = FALSE, chulls = FALSE, paths = NULL)
Output
  your_phyloseq %>%
   tax_transform(rank = "Genus", trans = "identity") %>%
   ord_calc(
    method = "RDA"
   ) %>% 
   ord_plot(
    axes = c(1, 2),
    colour = "v", fill = "v",
    shape = "var", alpha = "aVariable",
    size = 1
   )

Code
  for (x in list(p, a, c)) cat(x, "\t")
Output
  FALSE     aVariable   test1 test2     
Code
  ord_code(rank = "Genus", trans = "identity", dist = "none", ord = "RDA", const = c,
    conds = NULL, x = 1, y = 2, colour = "v", fill = "v", shape = "var", alpha = a,
    size = 1, plot_taxa = p, ellipses = FALSE, chulls = FALSE, paths = NULL)
Output
  your_phyloseq %>%
   tax_transform(rank = "Genus", trans = "identity") %>%
   ord_calc(
    constraints = c("test1", "test2"),
    method = "RDA"
   ) %>% 
   ord_plot(
    axes = c(1, 2),
    colour = "v", fill = "v",
    shape = "var", alpha = "aVariable",
    size = 1
   )

Code
  for (x in list(p, a, c)) cat(x, "\t")
Output
  1 2 3 4 5 6   0.5         
Code
  ord_code(rank = "Genus", trans = "identity", dist = "none", ord = "RDA", const = c,
    conds = NULL, x = 1, y = 2, colour = "v", fill = "v", shape = "var", alpha = a,
    size = 1, plot_taxa = p, ellipses = FALSE, chulls = FALSE, paths = NULL)
Output
  your_phyloseq %>%
   tax_transform(rank = "Genus", trans = "identity") %>%
   ord_calc(
    method = "RDA"
   ) %>% 
   ord_plot(
    axes = c(1, 2),
    plot_taxa = 1:6,
    colour = "v", fill = "v",
    shape = "var", alpha = 0.5,
    size = 1
   )

Code
  for (x in list(p, a, c)) cat(x, "\t")
Output
  1 2 3 4 5 6   0.5     test1 test2     
Code
  ord_code(rank = "Genus", trans = "identity", dist = "none", ord = "RDA", const = c,
    conds = NULL, x = 1, y = 2, colour = "v", fill = "v", shape = "var", alpha = a,
    size = 1, plot_taxa = p, ellipses = FALSE, chulls = FALSE, paths = NULL)
Output
  your_phyloseq %>%
   tax_transform(rank = "Genus", trans = "identity") %>%
   ord_calc(
    constraints = c("test1", "test2"),
    method = "RDA"
   ) %>% 
   ord_plot(
    axes = c(1, 2),
    plot_taxa = 1:6,
    colour = "v", fill = "v",
    shape = "var", alpha = 0.5,
    size = 1
   )

Code
  for (x in list(p, a, c)) cat(x, "\t")
Output
  1 2 3 4 5 6   aVariable       
Code
  ord_code(rank = "Genus", trans = "identity", dist = "none", ord = "RDA", const = c,
    conds = NULL, x = 1, y = 2, colour = "v", fill = "v", shape = "var", alpha = a,
    size = 1, plot_taxa = p, ellipses = FALSE, chulls = FALSE, paths = NULL)
Output
  your_phyloseq %>%
   tax_transform(rank = "Genus", trans = "identity") %>%
   ord_calc(
    method = "RDA"
   ) %>% 
   ord_plot(
    axes = c(1, 2),
    plot_taxa = 1:6,
    colour = "v", fill = "v",
    shape = "var", alpha = "aVariable",
    size = 1
   )

Code
  for (x in list(p, a, c)) cat(x, "\t")
Output
  1 2 3 4 5 6   aVariable   test1 test2     
Code
  ord_code(rank = "Genus", trans = "identity", dist = "none", ord = "RDA", const = c,
    conds = NULL, x = 1, y = 2, colour = "v", fill = "v", shape = "var", alpha = a,
    size = 1, plot_taxa = p, ellipses = FALSE, chulls = FALSE, paths = NULL)
Output
  your_phyloseq %>%
   tax_transform(rank = "Genus", trans = "identity") %>%
   ord_calc(
    constraints = c("test1", "test2"),
    method = "RDA"
   ) %>% 
   ord_plot(
    axes = c(1, 2),
    plot_taxa = 1:6,
    colour = "v", fill = "v",
    shape = "var", alpha = "aVariable",
    size = 1
   )

ord_code_dist helper works

Code
  cat(ord_code_dist("aitchison"))
Output
   dist_calc(dist = "aitchison") %>%

Code
  cat(ord_code_dist("none"))

Testing ord_code_stat() different combinations of ellipses and chulls

Code
  cat(ord_code_stat(ellipses = TRUE, chulls = FALSE, colour = "aVar"))
Output
   ) +
   ggplot2::stat_ellipse(
    ggplot2::aes(colour = aVar)
   )

Code
  cat(ord_code_stat(ellipses = FALSE, chulls = FALSE, colour = "aVar"))
Output
   )

Code
  cat(ord_code_stat(ellipses = FALSE, chulls = TRUE, colour = "aVar"))
Output
   ) +
   stat_chull(
    ggplot2::aes(colour = aVar)
   )

Code
  cat(ord_code_stat(ellipses = TRUE, chulls = TRUE, colour = "aVar"))
Output
   ) +
   stat_chull(
    ggplot2::aes(colour = aVar)
   )

Testing ord_code_paths() with different all_vars options (string & vec)

Code
  cat(ord_code_paths(paths = list(colour = "aVar", id_var = "bVar", id_values = letters[
    1:4], all_vars = "aVar")))
Output
   ) %>%
   add_paths(
    id_var = "bVar", 
    id_values = c("a", "b", "c", "d"),
    mapping = ggplot2::aes(colour = aVar)
   )

Code
  cat(ord_code_paths(paths = list(colour = "aVar", id_var = "bVar", id_values = letters[
    1:4], all_vars = c("otherVar", "anotherVar"))))
Output
   ) %>%
   add_paths(
    id_var = "bVar", 
    id_values = c("a", "b", "c", "d"),
    colour = "aVar"
   )

ord_build works

Code
  ord_build(data = dietswap, rank = "Genus", trans = "identity", dist = "bray",
    method = "PCoA", constraints = NULL, conditions = NULL)
Output
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 130 taxa and 222 samples ]
  sample_data() Sample Data:       [ 222 samples by 8 sample variables ]
  tax_table()   Taxonomy Table:    [ 130 taxa by 3 taxonomic ranks ]

  psExtra info:
  tax_agg = "Genus" tax_trans = "identity"

  bray distance matrix of size 222 
  0.7639533 0.7851213 0.6680796 0.7699252 0.80507 ...

  ordination of class: capscale rda cca 
  capscale(formula = distance ~ 1, data = data)
  Ordination info:
  method = 'PCoA'

Code
  ord_build(data = dietswap, rank = "Genus", trans = "clr", dist = NA, method = "auto",
    constraints = NULL, conditions = NULL)
Output
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 130 taxa and 222 samples ]
  sample_data() Sample Data:       [ 222 samples by 8 sample variables ]
  tax_table()   Taxonomy Table:    [ 130 taxa by 3 taxonomic ranks ]

  otu_get(counts = TRUE)         [ 130 taxa and 222 samples ]

  psExtra info:
  tax_agg = "Genus" tax_trans = "clr"

  ordination of class: rda cca 
  rda(formula = OTU ~ 1, data = data)
  Ordination info:
  method = 'PCA'

ord_explore_palet_fun works

Code
  ord_explore_palet_fun(dietswap, "Genus")
Output
     Prevotella melaninogenica et rel.   Oscillospira guillermondii et rel. 
                             "#A6CEE3"                            "#1F78B4" 
          Bacteroides vulgatus et rel.        Clostridium cellulosi et rel. 
                             "#B2DF8A"                            "#33A02C" 
             Prevotella oralis et rel. Faecalibacterium prausnitzii et rel. 
                             "#FB9A99"                            "#E31A1C" 
        Sporobacter termitidis et rel.        Clostridium symbiosum et rel. 
                             "#FDBF6F"                            "#FF7F00" 
                    Allistipes et rel.     Clostridium orbiscindens et rel. 
                             "#CAB2D6"                            "#6A3D9A" 
      Subdoligranulum variable at rel.           Ruminococcus obeum et rel. 
                             "#FFFF99"                            "#B15928" 
        Butyrivibrio crossotus et rel.         Bacteroides fragilis et rel. 
                             "#1ff8ff"                            "#1B9E77" 
                           Akkermansia           Bacteroides ovatus et rel. 
                             "#D95F02"                            "#7570B3" 
    Parabacteroides distasonis et rel.        Dorea formicigenerans et rel. 
                             "#E7298A"                            "#66A61E" 
         Bacteroides uniformis et rel.                            Dialister 
                             "#E6AB02"                            "#A6761D" 
      Bryantella formatexigens et rel.           Uncultured Clostridiales I 
                             "#666666"                            "#4b6a53" 
          Coprococcus eutactus et rel.           Clostridium leptum et rel. 
                             "#b249d5"                            "#7edc45" 
        Clostridium sphenoides et rel.             Escherichia coli et rel. 
                             "#5c47b8"                            "#cfd251" 
           Streptococcus bovis et rel.          Uncultured Clostridiales II 
                             "#ff69b4"                            "#69c86c" 
                       Bifidobacterium    Anaerotruncus colihominis et rel. 
                             "#cd3e50"                            "#83d5af" 
     Lachnospira pectinoschiza et rel.          Anaerostipes caccae et rel. 
                             "#da6130"                            "#5e79b2" 
         Ruminococcus callidus et rel.      Bacteroides splachnicus et rel. 
                             "#c29545"                            "#532a5a" 
           Ruminococcus bromii et rel.          Prevotella tannerae et rel. 
                             "#5f7b35"                            "#c497cf" 
          Lachnobacillus bovis et rel.          Eubacterium rectale et rel. 
                             "#773a27"                            "#7cb9cb" 
        Mitsuokella multiacida et rel. Outgrouping clostridium cluster XIVa 
                             "#594e50"                            "#d3c4a8" 
            Clostridium nexile et rel.                                Other 
                             "#c17e7f"                             "grey90"

Code
  ord_explore_palet_fun(ps = dietswap, tax_level = "Family", top_by = median,
    other = "colourz")
Output
              Bacteroidetes    Clostridium cluster IV  Clostridium cluster XIVa 
                  "#A6CEE3"                 "#1F78B4"                 "#B2DF8A" 
             Proteobacteria    Clostridium cluster IX                   Bacilli 
                  "#33A02C"                 "#FB9A99"                 "#E31A1C" 
   Uncultured Clostridiales            Actinobacteria           Verrucomicrobia 
                  "#FDBF6F"                 "#FF7F00"                 "#CAB2D6" 
     Clostridium cluster XI     Clostridium cluster I   Clostridium cluster XVI 
                  "#6A3D9A"                 "#FFFF99"                 "#B15928" 
      Uncultured Mollicutes Clostridium cluster XVIII              Fusobacteria 
                  "#1ff8ff"                 "#1B9E77"                 "#D95F02" 
    Clostridium cluster III  Clostridium cluster XIII    Clostridium cluster XV 
                  "#7570B3"                 "#E7298A"                 "#66A61E" 
   Clostridium cluster XVII            Asteroleplasma              Spirochaetes 
                  "#E6AB02"                 "#A6761D"                 "#666666" 
              Cyanobacteria                     Other 
                  "#4b6a53"                 "colourz"


david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.

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