Preparing merge

src/GRaNIE/vignettes/workflow.R

@@ -150,11 +150,11 @@ GRN = GRaNIE::addConnections_TF_peak(GRN, plotDiagnosticPlots = TRUE,
 
 
 ## ---- echo=FALSE, fig.cap="<i>TF-enhancer diagnostic plots for the TF E2F6.0.A for real data</i>", out.width = '80%'----------------------------------------------------------
-knitr::include_graphics("figs/TFPeak_fdr_orig/p-39.png")
+knitr::include_graphics("figs/TFPeak_fdr_orig/p-40.png")
 
 
 ## ---- echo=FALSE, fig.cap="<i>TF-enhancer diagnostic plots for the TF E2F6.0.A for permuted data</i>", out.width = '80%'------------------------------------------------------
-knitr::include_graphics("figs/TFPeak_fdr_perm/p-39.png")
+knitr::include_graphics("figs/TFPeak_fdr_perm/p-40.png")
 
 
 ## ----runARClassification, echo=TRUE, include=TRUE, eval = TRUE, class.output="scroll-200"-------------------------------------------------------------------------------------
@@ -225,15 +225,15 @@ GRN = GRaNIE::plot_stats_connectionSummary(GRN, type = "heatmap", forceRerun = T
 GRN = GRaNIE::plot_stats_connectionSummary(GRN, type = "boxplot", forceRerun = TRUE)
 
 
-## ---- echo=FALSE, fig.cap="<i>Filtered eGRN connection summary (heatmap) for TFs</i>", out.width = '60%'----------------------------------------------------------------------
+## ---- echo=FALSE, fig.cap="<i>Filtered eGRN connection summary (heatmap) for TFs</i>", out.width = '75%'----------------------------------------------------------------------
 knitr::include_graphics("figs/connectionsHeatmap/p-1.png")
 
 
-## ---- echo=FALSE, fig.cap="<i>Filtered eGRN connection summary (heatmap) for enhancers</i>", out.width = '60%'----------------------------------------------------------------
+## ---- echo=FALSE, fig.cap="<i>Filtered eGRN connection summary (heatmap) for enhancers</i>", out.width = '75%'----------------------------------------------------------------
 knitr::include_graphics("figs/connectionsHeatmap/p-2.png")
 
 
-## ---- echo=FALSE, fig.cap="<i>Filtered eGRN connection summary (heatmap) for genes</i>", out.width = '60%'--------------------------------------------------------------------
+## ---- echo=FALSE, fig.cap="<i>Filtered eGRN connection summary (heatmap) for genes</i>", out.width = '75%'--------------------------------------------------------------------
 knitr::include_graphics("figs/connectionsHeatmap/p-3.png")
 
 
@@ -274,19 +274,19 @@ knitr::include_graphics("figs/enrichment.community/p-01.png")
 
 
 ## ---- echo=FALSE, fig.cap="<i>GO term enrichment results for individual communities</i>", out.width = '100%'------------------------------------------------------------------
-knitr::include_graphics("figs/enrichment.community/p-04.png")
+knitr::include_graphics("figs/enrichment.community/p-02.png")
 
 
 ## ---- echo=FALSE, fig.cap="<i>GO term enrichment results for individual communities</i>", out.width = '100%'------------------------------------------------------------------
-knitr::include_graphics("figs/enrichment.community/p-03.png")
+knitr::include_graphics("figs/enrichment.community/p-09.png")
 
 
 ## ---- echo=FALSE, fig.cap="<i>Enrichment summary and comparison across communities and the whole network</i>", out.width = '100%'---------------------------------------------
-knitr::include_graphics("figs/enrichment.community/p-19.png")
+knitr::include_graphics("figs/enrichment.community/p-07.png")
 
 
 ## ---- echo=FALSE, fig.cap="<i>Enrichment summary and comparison across communities and the whole network</i>", out.width = '100%'---------------------------------------------
-knitr::include_graphics("figs/enrichment.community/p-20.png")
+knitr::include_graphics("figs/enrichment.community/p-08.png")
 
 
 ## ----saveObject3, echo=TRUE, include=TRUE, class.output="scroll-200"----------------------------------------------------------------------------------------------------------