Plots and themes
Last updated: 2022-02-28
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Knit directory: STUtility_web_site/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 0dafcee | Ludvig Larsson | 2021-05-06 | Build site. |
| Rmd | b7a0414 | Ludvig Larsson | 2021-05-06 | Updated tutorials |
Patchwork
Many of the plots generated with vsiualization functions from STutility are built using the patchwork R package. This package makes it much easier to change the layout and themes of different plots and we’ll go through a couple of examples here.
Let’s draw a spatial distribution of Pvalb and Th using ST.FeaturePlot and a violin plot showing the expression of these genes within each clusters.
Some of the layout options can be controlled direclty from ST.FeaturePlot using for example ncol and grid.ncol, but you can also rearrange the plot afterwards. Here we set ncol = 2 to specify that the sections will be arranged in two columns and grid.ncol = 1 to specify that the features will be arranged in 1 column.
p1 <- ST.FeaturePlot(se, features = c("Pvalb", "Th"), ncol = 2, grid.ncol = 1)
p1
| Version | Author | Date |
|---|---|---|
| 0dafcee | Ludvig Larsson | 2021-05-06 |
Now let’s add a violin plot and show it side by side with the spatial feature plot.
p2 <- VlnPlot(se, features = c("Pvalb", "Th"), ncol = 1, group.by = "seurat_clusters")
p1 - p2
| Version | Author | Date |
|---|---|---|
| 0dafcee | Ludvig Larsson | 2021-05-06 |
As you can see, it is very easy to combine plots side by side. If you want the sub plots to take up more or less area of the total plot, you can specify layout options with the patchwork function plot_layout.
p1 <- ST.FeaturePlot(se, features = c("Pvalb", "Th"), grid.ncol = 1, indices = 1)
p2 <- VlnPlot(se, features = c("Pvalb", "Th"), ncol = 1, group.by = "seurat_clusters")
# Give the second plot with a width that is 2x the width of the first
p1 - p2 + patchwork::plot_layout(widths = c(1, 2))
| Version | Author | Date |
|---|---|---|
| 0dafcee | Ludvig Larsson | 2021-05-06 |
Or an even more complex example
p3 <- ST.FeaturePlot(se, features = c("Pvalb", "Th"), ncol = 2, grid.ncol = 2, show.sb = FALSE)
p1 <- FeaturePlot(se, features = c("Pvalb", "Th"), cols = c("mistyrose", "red", "darkred"))
p2 <- VlnPlot(se, features = c("Pvalb", "Th"), ncol = 2, group.by = "seurat_clusters")
(p1 - p2)/p3
| Version | Author | Date |
|---|---|---|
| 0dafcee | Ludvig Larsson | 2021-05-06 |
Themes
It is also easy to change the theme of your plots, even after it has been drawn. You can specify a custom theme using the custom.theme argument in ST.FeaturePlot, FeatureOverlay, etc. But it’s even easier with the patchwork system.
custom_theme <- theme(legend.position = c(0.45, 0.8), # Move color legend to top
legend.direction = "horizontal", # Flip legend
legend.text = element_text(angle = 30, hjust = 1), # rotate legend axis text
strip.text = element_blank(), # remove strip text
plot.title = element_blank(), # remove plot title
plot.margin = margin(t = 0, r = 0, b = 0, l = 0, unit = "cm")) # remove plot margins
p <- ST.FeaturePlot(se, features = "nFeature_RNA", ncol = 2, show.sb = FALSE, palette = "Spectral")
p & custom_theme
| Version | Author | Date |
|---|---|---|
| 0dafcee | Ludvig Larsson | 2021-05-06 |
Or you can for example add a grid to show the x/y axes. Here, the x/y axes reoresent the pixel coordinates mapped to the “tissue_hires_image.png” from the spaceranger output.
p & theme_bw()
| Version | Author | Date |
|---|---|---|
| 0dafcee | Ludvig Larsson | 2021-05-06 |
A work by Joseph Bergenstråhle and Ludvig Larsson
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS/LAPACK: /Users/ludviglarsson/anaconda3/envs/R4.0/lib/libopenblasp-r0.3.12.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] magrittr_2.0.1 kableExtra_1.3.4 STutility_0.1.0 ggplot2_3.3.5
[5] SeuratObject_4.0.0 Seurat_4.0.2 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] utf8_1.2.1 reticulate_1.18 tidyselect_1.1.1
[4] htmlwidgets_1.5.3 grid_4.0.3 Rtsne_0.15
[7] munsell_0.5.0 codetools_0.2-18 ica_1.0-2
[10] units_0.7-1 future_1.21.0 miniUI_0.1.1.1
[13] withr_2.4.1 colorspace_2.0-0 highr_0.8
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[19] ROCR_1.0-11 tensor_1.5 listenv_0.8.0
[22] labeling_0.4.2 git2r_0.28.0 polyclip_1.10-0
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[58] abind_1.4-5 crosstalk_1.1.1 httpuv_1.5.5
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[76] rpart_4.1-15 dbscan_1.1-6 deldir_1.0-6
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[82] zoo_1.8-9 ggrepel_0.9.1 cluster_2.1.1
[85] colorRamps_2.3 fs_1.5.0 data.table_1.14.0
[88] magick_2.7.2 scattermore_0.7 readbitmap_0.1.5
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[94] whisker_0.4 fitdistrplus_1.1-3 matrixStats_0.58.0
[97] patchwork_1.1.1 shinyjs_2.0.0 mime_0.10
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[127] plotly_4.9.3 spatstat.sparse_2.0-0 xml2_1.3.2
[130] foreach_1.5.1 svglite_2.0.0 bslib_0.2.4
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