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Update plotting_vignette.Rmd
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dimalvovs authored Dec 7, 2023
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8 changes: 4 additions & 4 deletions vignettes/plotting_vignette.Rmd
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Expand Up @@ -75,14 +75,14 @@ cor_heatmap(

`feat_heatmap()` is used to show the transcription factor activation for features in the signaling network.
```{r featheatmap}
feat_heatmap(dom)
feat_heatmap(dom, use_raster = FALSE)
```

It functions similarly to `cor_heatmap()`, with arguments to select a specific vector of features, to use a boolean view with a threshold, and to pass other arguments to `NMF::aheatmap()`. Specific to this function though are arguments for setting the range of values to be visualized and one to choose whether or not to normalize the scores to the max value.
```{r featheatmap-options, fig.show="hold", out.width = "50%", eval = FALSE}
```{r featheatmap-options, fig.show="hold", out.width = "50%"}
feat_heatmap(dom, min_thresh = 0.1, max_thresh = 0.6,
norm = TRUE, bool = FALSE)
feat_heatmap(dom, bool = TRUE)
norm = TRUE, bool = FALSE, use_raster = FALSE)
feat_heatmap(dom, bool = TRUE, use_raster = FALSE)
```

### Heatmap of Incoming Signaling for a Cluster
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