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Merge branch 'develop' into feat/AddAzimuthResults
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jaisonj708 authored May 7, 2021
2 parents 2d9b487 + c3bc3d5 commit 5a3c44e
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Package: Seurat
Version: 4.0.1.9008
Date: 2021-04-26
Version: 4.0.1.9010
Date: 2021-05-06
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Authors@R: c(
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2 changes: 2 additions & 0 deletions NEWS.md
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Expand Up @@ -16,6 +16,8 @@
- Fix `DotPlot` to use `log1p` when `scale=False`
([#4298](https://github.com/satijalab/seurat/issues/4298))
- Fix split and shuffled `DimPlot`
- Disallow NULL or another length 0 vector for `ident.1` in `FindMarkers()`
- Fix range shift when labeling clusters on a GeomSpatial plot

# Seurat 4.0.1 (2020-03-17)
## Added
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3 changes: 3 additions & 0 deletions R/differential_expression.R
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Expand Up @@ -813,6 +813,9 @@ FindMarkers.Seurat <- function(
if (!is.null(x = assay) && !is.null(x = reduction)) {
stop("Please only specify either assay or reduction.")
}
if (length(x = ident.1) == 0) {
stop("At least 1 ident must be specified in `ident.1`")
}
# select which data to use
if (is.null(x = reduction)) {
assay <- assay %||% DefaultAssay(object = object)
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6 changes: 6 additions & 0 deletions R/visualization.R
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Expand Up @@ -4694,6 +4694,8 @@ LabelClusters <- function(
}
pb <- ggplot_build(plot = plot)
if (geom == 'GeomSpatial') {
xrange.save <- layer_scales(plot = plot)$x$range$range
yrange.save <- layer_scales(plot = plot)$y$range$range
data[, xynames["y"]] = max(data[, xynames["y"]]) - data[, xynames["y"]] + min(data[, xynames["y"]])
if (!pb$plot$plot_env$crop) {
y.transform <- c(0, nrow(x = pb$plot$plot_env$image)) - pb$layout$panel_params[[1]]$y.range
Expand Down Expand Up @@ -4771,6 +4773,10 @@ LabelClusters <- function(
...
)
}
# restore old axis ranges
if (geom == 'GeomSpatial') {
plot <- suppressMessages(expr = plot + coord_fixed(xlim = xrange.save, ylim = yrange.save))
}
return(plot)
}

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