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Remove miaTime #98

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merged 5 commits into from
Oct 5, 2023
Merged

Remove miaTime #98

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TuomasBorman Oct 2, 2023
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TuomasBorman Oct 2, 2023
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TuomasBorman Oct 5, 2023
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Merge branch 'master' into remove_miatime
TuomasBorman Oct 5, 2023
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TuomasBorman Oct 5, 2023
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8 changes: 4 additions & 4 deletions vignettes/miaViz.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -256,7 +256,7 @@ plotColGraph(altExp(GlobalPatterns,"Genus"),

# Plotting of serial data

```{r}
```{r, eval=FALSE}
# Load data from miaTime package
library("miaTime")
data(SilvermanAGutData, package="miaTime")
Expand All @@ -271,7 +271,7 @@ descriptor for ordering the data. The `y` argument selects the feature to show.
Since plotting a lot of features is not advised a maximum of 20 features can
plotted at the same time.

```{r}
```{r, eval=FALSE}
plotSeries(tse,
x = "DAY_ORDER",
y = taxa,
Expand All @@ -281,7 +281,7 @@ If replicated data is present, data is automatically used for calculation of the
`mean` and `sd` and plotted as a range. Data from different assays can be used
for plotting via the `assay.type`.

```{r}
```{r, eval=FALSE}
plotSeries(tse[taxa,],
x = "DAY_ORDER",
colour_by = "Family",
Expand All @@ -291,7 +291,7 @@ plotSeries(tse[taxa,],

Additional variables can be used to modify line type aesthetics.

```{r}
```{r, eval=FALSE}
plotSeries(tse,
x = "DAY_ORDER",
y = getTopTaxa(tse, 5),
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