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V1.2.0
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Please find an end-to-end tutorial at [https://boyiguo1.github.io/escheR/](https://boyiguo1.github.io/escheR/articles/SRT_eg.html) | ||
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## Syntax | ||
![](man/figures/escheR_syntax.pdf) | ||
![](man/figures/syntax.png) | ||
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# Frequently Asked Questions | ||
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* Can I use `escheR` on `SingleCellExperiment` object? | ||
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Yes. Starting from Version 1.2.0, `escheR` supports the visualization of | ||
dimensionality reduced embeddings of a `SingleCellExperiment` object by | ||
providing values to the argument `dimred`. For more information, please see | ||
[Beyond Sequence-based Spatially-Resolved Data](https://boyi-guo.com/escheR/articles/more_than_visium.html#visualized-dimensionality-reduced-embedding-with-singlecellexperiment). | ||
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* How can I make plots to visualize dimensional reduced embeddings? | ||
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* Can I highlight only one group/level of a multi-level categorical variables? | ||
Yes, you can provide a string value to the`dimred` argument. The string value | ||
should be included in `reducedDimNames(object)`. For more information, please | ||
see [Beyond Sequence-based Spatially-Resolved Data](https://boyi-guo.com/escheR/articles/more_than_visium.html#visualized-dimensionality-reduced-embedding-with-singlecellexperiment). | ||
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* Can I highlight only a subset of groups/levels for a categorical variables? | ||
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Yes, please find the example in [Adjusting aesthetics](https://boyi-guo.com/escheR/articles/SRT_eg.html#adjusting-aesthetics). | ||
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* Can `escheR` be directly applied to `Seurat` or `Giotto` objects? | ||
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Unfortunately, `Seurat` or `Giotto` objects can not be directly pipe into | ||
`make_escheR` function. Instead, we provide a generic function that works | ||
with a `data.frame` object as input. Please find example via [Beyond Bioconductor Eco-system](https://boyi-guo.com/escheR/articles/more_than_visium.html#beyond-bioconductor-eco-system). | ||
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* How can I make a paneled figure containing multiple `escheR` plots? | ||
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You can compile and arrange individual plots by `escheR` via functions, e.g. [`cowplot::plot_grid`](https://wilkelab.org/cowplot/articles/plot_grid.html), [`patchwork`](https://patchwork.data-imaginist.com/index.html). Please find the | ||
example via [Plot Multiple Samples](https://boyi-guo.com/escheR/articles/SRT_eg.html#plot-multiple-samples). | ||
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* How can I choose color palettes for `add_fill` and `add_ground` to minimize interference? | ||
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Interested user can explore the topic on bivariate color palette. The [blog post](https://jakubnowosad.com/posts/2020-08-25-cbc-bp2/) by Jakub Nowosad and R package [`biscale`](https://cran.r-project.org/web/packages/biscale/vignettes/bivariate_palettes.html) could be helpful. | ||
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* Can I apply `escheR` to plot image-based spatially resolved data? | ||
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In principle, `escheR` can be used to visualize image-based spatially-resolved (SR) | ||
data. See examples via [Image-based SpatialExperiment Object](https://boyi-guo.com/escheR/articles/more_than_visium.html#image-based-spatialexperiment-object). | ||
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Nevertheless, we are still optimizing the design principles for image-based SR | ||
data due to the difference in throughput compared to the sequence-based | ||
spatially resolved data. Optimization for image-based SR data visualization | ||
will be the main focus of our upcoming updates. We are open to working with | ||
new ideas and seek collaboration. | ||
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* Can I plot polygons as each data points to show cell morphology? | ||
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Unfortunately, not now. We acknowledge it would be a very important feature to | ||
consider, and we are motivated to implement it in our future updates. | ||
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# Citation | ||
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Our preprint describing `escheR` is available from bioRxiv: | ||
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