Commit 3e06690d authored by Christian Arnold's avatar Christian Arnold
Browse files

Preparing merge

parent 9955e64b
Pipeline #29499 passed with stage
in 30 seconds
......@@ -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"----------------------------------------------------------------------------------------------------------
......
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