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grunwaldlab · May 17, 2017 · 984bbb2 · 984bbb2
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diff --git a/scratch/arrange_taxa_gc_weirdness.Rmd b/scratch/arrange_taxa_gc_weirdness.Rmd
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+
+
+
+```{r}
+install.packages("metacoder")
+library(metacoder)
+gctorture2(999)
+#> [1] 0
+arrange_taxa(unite_ex_data_3, desc(name))
+#> Error in data[, colnames(data) %in% col_subset, drop = FALSE]: incorrect number of dimensions
+```
+
+
+## old metacoder, new dplyr
+
+```{r}
+install.packages("metacoder")
+devtools::install_github("tidyverse/dplyr@v0.6.0-rc")
+library(metacoder)
+arrange_taxa(unite_ex_data_3, desc(name))
+```
+
+
+## new metacoder, old dplyr
+
+```{r}
+devtools::install_github("grunwaldlab/metacoder@dev")
+devtools::install_github("tidyverse/dplyr@v0.5.0")
+library(metacoder)
+arrange_taxa(unite_ex_data_3, desc(name))
+```
diff --git a/scratch/example.phyloseq b/scratch/example.phyloseq
diff --git a/scratch/issue_123--warning_for_invalid_class_regex.Rmd b/scratch/issue_123--warning_for_invalid_class_regex.Rmd
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+
+## Reproduce error
+
+```{r, eval = FALSE}
+devtools::install_github("grunwaldlab/metacoder@59c6555")
+```
+
+
+```{r}
+library(metacoder)
+file_path <- system.file("extdata", "unite_general_release.fasta", package = "metacoder")
+sequences <- ape::read.FASTA(file_path)
+unite_ex_data_3 <- extract_taxonomy(sequences,
+                                    regex = "^(.*)\\|(.*)\\|(.*)\\|.*\\|(.*)$",
+                                    key = c(seq_name = "obs_info", seq_id = "obs_info",
+                                            other_id = "obs_info", "class"),
+                                    class_regex = "^(.*)_not_here_(.*)$",
+                                    class_key = c(unite_rank = "taxon_info", "name"),
+                                    class_sep = ";")
+```
+
+
+## Verify fix
+
+
diff --git a/scratch/issue_140.Rmd b/scratch/issue_140.Rmd
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+```{r}
+library(metacoder)
+heat_tree(unite_ex_data_3, node_size = n_obs, node_label = name, node_color = ifelse(n_supertaxa == 2, "red", "grey"))
+heat_tree(unite_ex_data_3, node_size = n_obs, node_label = name, node_color = ifelse(n_supertaxa %in% 2:5, n_obs, "grey"))
+```
+