fix: bug fix for v0.9.1

adrientaudiere · Apr 28, 2024 · 9860e25 · 9860e25
1 parent 4c0082e
commit 9860e25
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Showing 26 changed files with 131 additions and 123 deletions.
diff --git a/R/plot_functions.R b/R/plot_functions.R
@@ -1471,17 +1471,19 @@ hill_pq <- function(physeq,
         "You must set only one parameter of variable or fact. This 2
         parameters are strictly equivalent."
       )
+    } else {
+      variable_fac <- variable
     }
   } else {
     if (!is.null(fact)) {
-      variable <- fact
+      variable_fac <- fact
     } else {
       stop("You must set the parameter fact.")
     }
   }
-  var <- sym(variable)
+  var <- sym(variable_fac)
   if (is.na(color_fac)) {
-    color_fac <- sym(variable)
+    color_fac <- sym(variable_fac)
   } else {
     color_fac <- sym(color_fac)
   }
@@ -1507,7 +1509,7 @@ hill_pq <- function(physeq,
   p_var <-
     hill_tuckey_pq(
       physeq,
-      modality = variable,
+      modality = variable_fac,
       hill_scales = hill_scales,
       correction_for_sample_size = correction_for_sample_size
     )
@@ -1525,9 +1527,9 @@ hill_pq <- function(physeq,
       subtitle_plot <- paste0(
         "Nb of samples: '",
         paste0(
-          names(table(physeq@sam_data[[variable]])),
+          names(table(physeq@sam_data[[variable_fac]])),
           sep = "' : ",
-          table(physeq@sam_data[[variable]]),
+          table(physeq@sam_data[[variable_fac]]),
           collapse = " - '"
         )
       )

diff --git a/README.Rmd b/README.Rmd
@@ -87,7 +87,7 @@ summary_plot_pq(data_fungi)
 ### Alpha-diversity analysis
 
 ```{r, fig.cap="Hill number 1"}
-p <- MiscMetabar::hill_pq(data_fungi, variable = "Height")
+p <- MiscMetabar::hill_pq(data_fungi, fact = "Height")
 p$plot_Hill_0
 ```
 

diff --git a/README.md b/README.md
@@ -117,32 +117,16 @@ summary_plot_pq(data_fungi)
 ### Alpha-diversity analysis
 
 ``` r
-p <- MiscMetabar::hill_pq(data_fungi, variable = "Height")
+p <- MiscMetabar::hill_pq(data_fungi, fact = "Height")
 p$plot_Hill_0
+#> NULL
 ```
 
-<div class="figure">
-
-<img src="man/figures/README-unnamed-chunk-5-1.png" alt="Hill number 1" width="100%" />
-<p class="caption">
-Hill number 1
-</p>
-
-</div>
-
 ``` r
 p$plot_tuckey
+#> NULL
 ```
 
-<div class="figure">
-
-<img src="man/figures/README-unnamed-chunk-6-1.png" alt="Result of the Tuckey post-hoc test" width="100%" />
-<p class="caption">
-Result of the Tuckey post-hoc test
-</p>
-
-</div>
-
 ### Beta-diversity analysis
 
 ``` r

diff --git a/docs/articles/MiscMetabar.html b/docs/articles/MiscMetabar.html
diff --git a/docs/articles/Reclustering.html b/docs/articles/Reclustering.html
diff --git a/docs/articles/Reclustering_files/figure-html/unnamed-chunk-4-2.png b/docs/articles/Reclustering_files/figure-html/unnamed-chunk-4-2.png
diff --git a/docs/articles/alpha-div_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/alpha-div_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -13,7 +13,7 @@ articles:
   states_of_fields_in_R: states_of_fields_in_R.html
   tengeler: tengeler.html
   tree_visualization: tree_visualization.html
-last_built: 2024-04-26T13:02Z
+last_built: 2024-04-28T13:37Z
 urls:
   reference: https://adrientaudiere.github.io/MiscMetabar/reference
   article: https://adrientaudiere.github.io/MiscMetabar/articles

diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png
diff --git a/docs/reference/SRS_curve_pq-1.png b/docs/reference/SRS_curve_pq-1.png
diff --git a/docs/reference/accu_plot-1.png b/docs/reference/accu_plot-1.png
diff --git a/docs/reference/accu_plot-2.png b/docs/reference/accu_plot-2.png
diff --git a/docs/reference/accu_plot.html b/docs/reference/accu_plot.html
diff --git a/docs/reference/asv2otu.html b/docs/reference/asv2otu.html