diff --git a/DESeq2_markdown_GH_git_out.md b/DESeq2_markdown_GH_git_out.md index 40e3a86..deb16a7 100644 --- a/DESeq2_markdown_GH_git_out.md +++ b/DESeq2_markdown_GH_git_out.md @@ -309,7 +309,8 @@ plotPCA.3d <- function (object, intgroup = "condition", ntop = 500, returnData = plotPCA.3d(normalizedBes17Short) ``` -![Besselfjord 3D PCA](Bess3d.png) +![Besselfjord 3D +PCA](./DESeq2_markdown_GH_git_out_files/figure-gfm/Bess3d.png) ## Results @@ -435,7 +436,7 @@ mat = GO_similarity(go_id, ont = "BP") df = simplifyGO(mat, fontsize_range = c(10,18), min_term = 1, draw_word_cloud = T) ``` - ## Cluster 7 terms by 'binary_cut'... 3 clusters, used 0.03349113 secs. + ## Cluster 7 terms by 'binary_cut'... 3 clusters, used 0.02066708 secs. Depending on the number of GO terms and clusters, the default plotting diff --git a/Bess3d.png b/DESeq2_markdown_GH_git_out_files/figure-gfm/Bess3d.png similarity index 100% rename from Bess3d.png rename to DESeq2_markdown_GH_git_out_files/figure-gfm/Bess3d.png diff --git a/DESeq2_markdown_GH_git_out_files/figure-gfm/GO vis-1.png b/DESeq2_markdown_GH_git_out_files/figure-gfm/GO vis-1.png index 3e74f9d..aec0a7c 100644 Binary files a/DESeq2_markdown_GH_git_out_files/figure-gfm/GO vis-1.png and b/DESeq2_markdown_GH_git_out_files/figure-gfm/GO vis-1.png differ diff --git a/DESeq2_markdown_GH_git_out_files/figure-gfm/outlier remake-1.png b/DESeq2_markdown_GH_git_out_files/figure-gfm/outlier remake-1.png index 9443471..fed25e9 100644 Binary files a/DESeq2_markdown_GH_git_out_files/figure-gfm/outlier remake-1.png and b/DESeq2_markdown_GH_git_out_files/figure-gfm/outlier remake-1.png differ diff --git a/DESeq2_markdown_GH_git_out_files/figure-gfm/sample distance-1.png b/DESeq2_markdown_GH_git_out_files/figure-gfm/sample distance-1.png index 18b06ef..9dc9c23 100644 Binary files a/DESeq2_markdown_GH_git_out_files/figure-gfm/sample distance-1.png and b/DESeq2_markdown_GH_git_out_files/figure-gfm/sample distance-1.png differ