update README

Luponsky · May 15, 2019 · a401e91 · a401e91
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diff --git a/R/plot_stacked_bar.R b/R/plot_stacked_bar.R
@@ -100,8 +100,10 @@ plot_stacked_bar <- function(phyloseq = NULL, level = NA, feature = NA,
         # Join metadata
         left_join(sample_feature) %>%
         # Group by feature parameter
+        # group_by_() can pass variable to group_by()
         group_by_(feature) %>%
         # Arrange order by total abundance and by group
+        # Set .by_group = TRUE to arrange by group
         arrange(desc(total), .by_group = TRUE) %>%
         select(-total)
       levels_SampleID <- plot_tab$SampleID

diff --git a/README.Rmd b/README.Rmd
@@ -79,17 +79,44 @@ track_reads_dada2(demo_dada2_result$reads_track, single_end = FALSE,
 
 # Stacked barplot of phylogenetic composition
 
-Use plot_stacked_bar function to plot the Family level abundance in every sample. You can change the 'level' argument to plot abundance in different level, or change the 'feature' to choose different feature you want to show in x-axis.
+Use plot_stacked_bar function to plot the taxonomy level abundance in every sample. You can change the 'level' argument to plot abundance in different level, or change the 'feature' to choose different feature you want to show in x-axis.
 
-Note: 
+### Minimum usage
+
+```{r Stacked barplot 1, fig.height=10}
+plot_stacked_bar(phyloseq = demo_phyloseq_object, level = "Family")
+```
+
+### Plot in relative abundance
+
+```{r Stacked barplot 2, fig.height=10}
+plot_stacked_bar(phyloseq = demo_phyloseq_object, level = "Family", 
+                 relative_abundance = TRUE)
+```
 
-If the legend is too much to show, set legend_position to "none".
+### If legends are too many to show, set legend_position to "none"
+
+```{r Stacked barplot 3, fig.height=10}
+plot_stacked_bar(phyloseq = demo_phyloseq_object, level = "Family", 
+                 legend_position = "none")
+```
+
+### If you want to show feature information in x-axis, set "feature" parameter
+
+```{r Stacked barplot 4, fig.height=10}
+plot_stacked_bar(phyloseq = demo_phyloseq_object, level = "Family", 
+                 legend_position = "none", 
+                 feature = "diagnosis")
+```
 
-### Family level
+### If you want the sample in specific order, pass ordered sample names to "order" parameter
 
-```{r Stacked barplot, fig.height=10}
+```{r Stacked barplot 5, fig.height=10}
+sample_order <- sample_names(demo_phyloseq_object)
 plot_stacked_bar(phyloseq = demo_phyloseq_object, level = "Family", 
-                 feature = "diagnosis", legend_position = "top")
+                 legend_position = "none", 
+                 feature = "diagnosis", 
+                 order = sample_order)
 ```
 
 # Alpha diversity

diff --git a/README.md b/README.md
@@ -92,20 +92,55 @@ track_reads_dada2(demo_dada2_result$reads_track, single_end = FALSE,
 Stacked barplot of phylogenetic composition
 ===========================================
 
-Use plot\_stacked\_bar function to plot the Family level abundance in every sample. You can change the 'level' argument to plot abundance in different level, or change the 'feature' to choose different feature you want to show in x-axis.
+Use plot\_stacked\_bar function to plot the taxonomy level abundance in every sample. You can change the 'level' argument to plot abundance in different level, or change the 'feature' to choose different feature you want to show in x-axis.
 
-Note:
+### Minimum usage
+
+``` r
+plot_stacked_bar(phyloseq = demo_phyloseq_object, level = "Family")
+```
+
+![](README_files/figure-markdown_github/Stacked%20barplot%201-1.png)
+
+### Plot in relative abundance
+
+``` r
+plot_stacked_bar(phyloseq = demo_phyloseq_object, level = "Family", 
+                 relative_abundance = TRUE)
+```
+
+![](README_files/figure-markdown_github/Stacked%20barplot%202-1.png)
+
+### If legends are too many to show, set legend\_position to "none"
+
+``` r
+plot_stacked_bar(phyloseq = demo_phyloseq_object, level = "Family", 
+                 legend_position = "none")
+```
+
+![](README_files/figure-markdown_github/Stacked%20barplot%203-1.png)
+
+### If you want to show feature information in x-axis, set "feature" parameter
+
+``` r
+plot_stacked_bar(phyloseq = demo_phyloseq_object, level = "Family", 
+                 legend_position = "none", 
+                 feature = "diagnosis")
+```
 
-If the legend is too much to show, set legend\_position to "none".
+![](README_files/figure-markdown_github/Stacked%20barplot%204-1.png)
 
-### Family level
+### If you want the sample in specific order, pass ordered sample names to "order" parameter
 
 ``` r
+sample_order <- sample_names(demo_phyloseq_object)
 plot_stacked_bar(phyloseq = demo_phyloseq_object, level = "Family", 
-                 feature = "diagnosis", legend_position = "top")
+                 legend_position = "none", 
+                 feature = "diagnosis", 
+                 order = sample_order)
 ```
 
-![](README_files/figure-markdown_github/Stacked%20barplot-1.png)
+![](README_files/figure-markdown_github/Stacked%20barplot%205-1.png)
 
 Alpha diversity
 ===============

diff --git a/README_files/figure-markdown_github/Stacked barplot 1-1.png b/README_files/figure-markdown_github/Stacked barplot 1-1.png
diff --git a/README_files/figure-markdown_github/Stacked barplot 2-1.png b/README_files/figure-markdown_github/Stacked barplot 2-1.png
diff --git a/README_files/figure-markdown_github/Stacked barplot 3-1.png b/README_files/figure-markdown_github/Stacked barplot 3-1.png
diff --git a/README_files/figure-markdown_github/Stacked barplot 4-1.png b/README_files/figure-markdown_github/Stacked barplot 4-1.png
diff --git a/README_files/figure-markdown_github/Stacked barplot 5-1.png b/README_files/figure-markdown_github/Stacked barplot 5-1.png