Commit 0b26c50e authored by Olivier Rue's avatar Olivier Rue
Browse files

curation complete MEAT

parent 13ee9457
Pipeline #45097 passed with stage
in 19 seconds
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......@@ -215,7 +215,7 @@ p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
### Richness
```{r, eval=T}
p <- plot_richness(physeq = meat_all, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson", "Fisher"))
p <- plot_richness(physeq = meat_all, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson"))
p + geom_boxplot() + NULL
```
......@@ -306,14 +306,15 @@ ggplot(df %>% pivot_longer(cols = c(Initial, Final), names_to = "Step", values_t
```{r, eval=T}
p <- plot_composition(physeq = meat_all_final, taxaRank1 = "Kingdom", taxaSet1 = "Fungi", taxaRank2 = "Species", numberOfTaxa = 22, x = "Sample")
p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
p <- p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
p + theme(legend.position="bottom")
```
### Richness
```{r, eval=T}
p <- plot_richness(physeq = meat_all_final, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson", "Fisher"))
p <- plot_richness(physeq = meat_all_final, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson"))
p + geom_boxplot() + NULL
```
......@@ -512,7 +513,7 @@ p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
### Richness
```{r, eval=T}
p <- plot_richness(physeq = cheese_all, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson", "Fisher"))
p <- plot_richness(physeq = cheese_all, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson"))
p + geom_boxplot() + NULL
```
......@@ -643,7 +644,7 @@ p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
### Richness
```{r, eval=T}
p <- plot_richness(physeq = cheese_all_final, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson", "Fisher"))
p <- plot_richness(physeq = cheese_all_final, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson"))
p + geom_boxplot() + NULL
```
......@@ -830,7 +831,7 @@ p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
### Richness
```{r, eval=T}
p <- plot_richness(physeq = bread_all, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson", "Fisher"))
p <- plot_richness(physeq = bread_all, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson"))
p + geom_boxplot() + NULL
```
......@@ -920,7 +921,7 @@ p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
### Richness
```{r, eval=F}
p <- plot_richness(physeq = bread_all_final, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson", "Fisher"))
p <- plot_richness(physeq = bread_all_final, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson"))
p + geom_boxplot() + NULL
```
......@@ -1097,7 +1098,7 @@ p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
### Richness
```{r, eval=T}
p <- plot_richness(physeq = wine_all, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson", "Fisher"))
p <- plot_richness(physeq = wine_all, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson"))
p + geom_boxplot() + NULL
```
......@@ -1187,7 +1188,7 @@ p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
### Richness
```{r, eval=F}
p <- plot_richness(physeq = bread_all_final, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson", "Fisher"))
p <- plot_richness(physeq = bread_all_final, x = "Marker", color = "Marker", shape = NULL, title = "Alpha diversity graphics", measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson"))
p + geom_boxplot() + NULL
```
......
This diff is collapsed.
......@@ -23,6 +23,7 @@ window.initializeCodeFolding = function(show) {
// create a collapsable div to wrap the code in
var div = $('<div class="collapse r-code-collapse"></div>');
var showThis = (show || $(this).hasClass('fold-show')) && !$(this).hasClass('fold-hide');
if (showThis) div.addClass('in');
var id = 'rcode-643E0F36' + currentIndex++;
div.attr('id', id);
$(this).before(div);
......@@ -30,7 +31,7 @@ window.initializeCodeFolding = function(show) {
// add a show code button right above
var showCodeText = $('<span>' + (showThis ? 'Hide' : 'Code') + '</span>');
var showCodeButton = $('<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm code-folding-btn pull-right float-right"></button>');
var showCodeButton = $('<button type="button" class="btn btn-default btn-xs code-folding-btn pull-right"></button>');
showCodeButton.append(showCodeText);
showCodeButton
.attr('data-toggle', 'collapse')
......@@ -46,27 +47,13 @@ window.initializeCodeFolding = function(show) {
div.before(buttonRow);
// show the div if necessary
if (showThis) div.collapse('show');
// update state of button on show/hide
// * Change text
// * add a class for intermediate states styling
div.on('hide.bs.collapse', function () {
showCodeText.text('Code');
showCodeButton.addClass('btn-collapsing');
});
div.on('hidden.bs.collapse', function () {
showCodeButton.removeClass('btn-collapsing');
showCodeText.text('Code');
});
div.on('show.bs.collapse', function () {
showCodeText.text('Hide');
showCodeButton.addClass('btn-expanding');
});
div.on('shown.bs.collapse', function () {
showCodeButton.removeClass('btn-expanding');
});
});
}
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