docs(MarkersPlot): update examples and references for pancreas_sub dataset

- Updated example data from pbmc_small to pancreas_sub
- Adjusted example calls for MarkersPlot with new parameters
- Changed documentation links from VolcanoPlot to MarkersPlot

Author: pwwang

R/markersplot.R

@@ -63,20 +63,20 @@
 #' * For `jitter`, `jitter_log2fc`, `jitter_pct`, the arguments will be passed to [plotthis::JitterPlot()]
 #' @examples
 #' \donttest{
-#' data("pbmc_small", package = "SeuratObject")
-#' markers <- Seurat::FindMarkers(pbmc_small,
-#'  group.by = "groups", ident.1 = "g1", ident.2 = "g2")
-#' allmarkers <- Seurat::FindAllMarkers(pbmc_small)  # RNA_snn_res.1
+#' data(pancreas_sub)
+#' markers <- Seurat::FindMarkers(pancreas_sub,
+#'  group.by = "Phase", ident.1 = "G2M", ident.2 = "G1")
+#' allmarkers <- Seurat::FindAllMarkers(pancreas_sub)  # seurat_clusters
 #'
-#' MarkersPlot(markers, p_adjust = FALSE)
-#' MarkersPlot(markers, p_adjust = FALSE, x_cutoff = 1)
+#' MarkersPlot(markers)
+#' MarkersPlot(markers, x_cutoff = 2)
 #' MarkersPlot(allmarkers, p_adjust = FALSE,
 #'     subset_by = "cluster", ncol = 2, subset_as_facet = TRUE)
-#' MarkersPlot(markers, p_adjust = FALSE, plot_type = "volcano_pct")
+#' MarkersPlot(markers, plot_type = "volcano_pct", flip_negative = TRUE)
 #'
 #' MarkersPlot(allmarkers, plot_type = "jitter", subset_by = "cluster")
 #' MarkersPlot(allmarkers, plot_type = "jitter_pct",
-#'     subset_by = "cluster", add_hline = 0)
+#'     subset_by = "cluster", add_hline = 0, shape = 16)
 #'
 #' MarkersPlot(allmarkers, plot_type = "heatmap_log2fc", subset_by = "cluster")
 #' MarkersPlot(allmarkers, plot_type = "heatmap_pct", subset_by = "cluster",
@@ -85,24 +85,25 @@
 #' MarkersPlot(allmarkers, plot_type = "dot_log2fc", subset_by = "cluster",
 #'     add_reticle = TRUE)
 #'
-#' MarkersPlot(allmarkers, object = pbmc_small, plot_type = "heatmap",
-#'     comparison_by = "cluster:RNA_snn_res.1")
+#' MarkersPlot(allmarkers, object = pancreas_sub, plot_type = "heatmap",
+#'    columns_split_by = "CellType",
+#'    comparison_by = "cluster:seurat_clusters")
 #'
 #' # Suppose we did a DE between g1 and g2 in each cluster
 #' allmarkers$comparison <- "g1:g2"
-#' MarkersPlot(allmarkers, object = pbmc_small, plot_type = "heatmap",
-#'    comparison_by = "comparison:groups", subset_by = "cluster:RNA_snn_res.1")
-#' MarkersPlot(allmarkers, object = pbmc_small, plot_type = "dot",
-#'    comparison_by = "comparison:groups", subset_by = "cluster:RNA_snn_res.1")
+#' MarkersPlot(allmarkers, object = pancreas_sub, plot_type = "heatmap",
+#'    comparison_by = "Phase", subset_by = "cluster:seurat_clusters")
+#' MarkersPlot(allmarkers, object = pancreas_sub, plot_type = "dot",
+#'    comparison_by = "Phase", subset_by = "cluster:seurat_clusters")
 #'
-#' MarkersPlot(allmarkers, object = pbmc_small, plot_type = "violin", select = 3,
-#'    comparison_by = "comparison:groups", subset_by = "cluster:RNA_snn_res.1")
+#' MarkersPlot(allmarkers, object = pancreas_sub, plot_type = "violin", select = 3,
+#'    comparison_by = "Phase", subset_by = "cluster:seurat_clusters")
 #'
-#' MarkersPlot(allmarkers, object = pbmc_small, plot_type = "box", select = 3,
-#'    comparison_by = "comparison:groups", subset_by = "cluster:RNA_snn_res.1")
+#' MarkersPlot(allmarkers, object = pancreas_sub, plot_type = "box", select = 3,
+#'    comparison_by = "Phase", subset_by = "cluster:seurat_clusters")
 #'
-#' MarkersPlot(allmarkers, object = pbmc_small, plot_type = "ridge", select = 2,
-#'    comparison_by = "comparison:groups", subset_by = "cluster:RNA_snn_res.1",
+#' MarkersPlot(allmarkers, object = pancreas_sub, plot_type = "ridge", select = 2,
+#'    comparison_by = "Phase", subset_by = "cluster:seurat_clusters",
 #'    ncol = 2)
 #' }
 #' @export

README.md

@@ -40,7 +40,7 @@ $ conda install pwwang::r-scplotter
 
 ![](./man/figures/gseaplot.png)
 
-[`VolcanoPlot`][9]
+[`MarkersPlot`][9]
 
 ![](./man/figures/volcanoplot.png)
 
@@ -106,7 +106,7 @@ chat$ask("Do a heatmap instead")
 [6]: https://pwwang.github.io/scplotter/reference/FeatureStatPlot.html
 [7]: https://pwwang.github.io/scplotter/reference/EnrichmentPlot.html
 [8]: https://pwwang.github.io/plotthis/reference/gsea.html
-[9]: https://pwwang.github.io/plotthis/reference/VolcanoPlot.html
+[9]: https://pwwang.github.io/scplotter/reference/MarkersPlot.html
 [10]: https://pwwang.github.io/scplotter/reference/CCCPlot.html
 [11]: https://pwwang.github.io/scplotter/reference/ClonalVolumePlot.html
 [12]: https://pwwang.github.io/scplotter/reference/ClonalAbundancePlot.html