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For work (single cell RNA-seq) I make and look at countless plots. Though most packages attempt to be colorblind-aware/friendly, I often find results uninterpretable when over a handful of colors are used. Some helpful strategies include: scatterHatch, adding different hatch patterns to clusters on top of colors; ggtrace; plotly interactivity; etc. But perhaps a simpler solution can be used – avoid using visually similar colors next to each other (ie. on a UMAP, neighboring clusters should never be light yellow and slightly darker yellow). In 1D plots (barplot, violin plots, etc), we’d simply pass a vector of dissimilar colors. Not so easy to do when 2D and many colors are involved. Hence this simple package.
# now on CRAN
install.packages("colorrepel")
# or latest devel version from github
devtools::install_github("https://github.com/raysinensis/color_repel")
library(colorrepel)
?gg_color_repel # overall wrapper function
a <- Seurat::DimPlot(so, group.by = "type", pt.size = 0.5)
b <- a + scale_color_manual(values = color_repel(a, sim = colorspace::tritan))
cowplot::plot_grid(a, b,
labels = c("original", "color_repel"))
a <- readRDS("bar_gg.rds")
b <- a + scale_fill_viridis_d(option = "H")
c <- b + scale_fill_manual(values = color_repel(b, col = "fill"))
# or use wrapper
c <- gg_color_repel(b, col = "fill")
cowplot::plot_grid(a,b,c, labels = c("default", "viridis", "color_repel"), nrow = 1)
a <- Seurat::DimPlot(so, group.by = "type", pt.size = 0.5)
b <- gg_color_repel(a, repel_label = T)
c <- gg_color_repel(a, encircle = T)
cowplot::plot_grid(b, c,
labels = c("label_repel", "encircle"))
Also see it in action here: https://raysinensis.shinyapps.io/spatialshiny_adr/
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In situ reconstruction of distinct normal and pathological cell populations within the human adrenal gland. Journal of the Endocrine Society, 2023. Fu R, Walters K, Kaufman M, Kocs K, Baldwin A, Kiseljak-Vassiliades K, Fishbein L, Mukherjee N. https://doi.org/10.1210/jendso/bvad131
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.