From 49dc5ab49ce556f6826cf996bc30a1a8c326d787 Mon Sep 17 00:00:00 2001 From: Bavanaa Date: Fri, 5 Jul 2024 15:21:20 -0700 Subject: [PATCH] shinyApp article image --- vignettes/articles/shiny_app.Rmd | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/vignettes/articles/shiny_app.Rmd b/vignettes/articles/shiny_app.Rmd index 3c78794..b0136f8 100755 --- a/vignettes/articles/shiny_app.Rmd +++ b/vignettes/articles/shiny_app.Rmd @@ -111,13 +111,14 @@ statistical significance (P value) versus magnitude of change (fold change). Here, the cutoffs for log2FC and P value can be adjusted to set thresholds for statistical significance. -![](images/VolcanoPlot.png){width=70%} +![](images/VolcanoPlot.png) ### Find Markers Marker features based on louvain/leiden cluster identities or cell metadata can be defined based on results of wilcoxon rank-sum test via [presto](https://www.biorxiv.org/content/10.1101/653253v1) or measures of cluster specificity with genesorteR (Ibrahim, 2020) . Variable numbers of marker genes per cell group can be specified based on adjusted p value and thresholded log fold change. -![](images/marker_gene_plot.png){width=70%} +![](images/marker_gene_plot.png) + ### Subset Seurat Input