Move methyl_mat assignment to visible code

nathansam · May 17, 2022 · f080bae · f080bae
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/_episodes/05-principal-component-analysis.md b/_episodes/05-principal-component-analysis.md
@@ -763,8 +763,8 @@ represents.
 > > 215281_x_at 0.003923775 0.003179556 -0.0004388192 9.664648e-05 0.003501335
 > >                    PC86        PC87          PC88         PC89         PC90
 > > 215281_x_at -0.00112973 0.006489667 -0.0005039785 -0.004296355 -0.002751513
-> >                    PC91
-> > 215281_x_at -0.01747638
+> >                   PC91
+> > 215281_x_at 0.01181236
 > > ~~~
 > > {: .output}
 > > 
@@ -826,8 +826,8 @@ represents.
 > > 211122_s_at 0.004995447 -0.008404118 0.00442875 -0.001027912 0.006104406
 > >                    PC82        PC83         PC84       PC85       PC86
 > > 211122_s_at -0.01988441 0.009667348 -0.008248781 0.01198369 0.01221713
-> >                     PC87        PC88        PC89        PC90        PC91
-> > 211122_s_at -0.003864842 -0.02876816 -0.01771452 -0.02164973 -0.02164521
+> >                     PC87        PC88        PC89        PC90       PC91
+> > 211122_s_at -0.003864842 -0.02876816 -0.01771452 -0.02164973 0.01215707
 > > ~~~
 > > {: .output}
 > > The function `pca` is used to perform PCA, and uses as inputs a matrix
@@ -946,7 +946,7 @@ biplot(pc, lab = rownames(pc$metadata), pointSize = 1, labSize = 1)
 
 
 ~~~
-Warning: ggrepel: 7 unlabeled data points (too many overlaps). Consider
+Warning: ggrepel: 6 unlabeled data points (too many overlaps). Consider
 increasing max.overlaps
 ~~~
 {: .warning}
@@ -967,7 +967,7 @@ plotloadings(pc, labSize = 3)
 
 
 ~~~
-Warning: ggrepel: 38 unlabeled data points (too many overlaps). Consider
+Warning: ggrepel: 35 unlabeled data points (too many overlaps). Consider
 increasing max.overlaps
 ~~~
 {: .warning}
@@ -998,7 +998,7 @@ detecting genes on each principal component.
 > > 
 > > 
 > > ~~~
-> > Warning: ggrepel: 35 unlabeled data points (too many overlaps). Consider
+> > Warning: ggrepel: 34 unlabeled data points (too many overlaps). Consider
 > > increasing max.overlaps
 > > ~~~
 > > {: .warning}

diff --git a/_episodes/07-non-metric-multidimensional-scaling.md b/_episodes/07-non-metric-multidimensional-scaling.md
@@ -503,7 +503,7 @@ Run 2 stress 0.1584647
 Run 3 stress 0.1611791 
 Run 4 stress 0.1789562 
 Run 5 stress 0.15668 
-Run 6 stress 0.1640325 
+Run 6 stress 0.1640326 
 Run 7 stress 0.148614 
 Run 8 stress 0.1519784 
 Run 9 stress 0.1443964 
@@ -513,18 +513,14 @@ Run 12 stress 0.1426428
 ... New best solution
 ... Procrustes: rmse 0.000483717  max resid 0.004997887 
 ... Similar to previous best
-Run 13 stress 0.1616122 
+Run 13 stress 0.1616121 
 Run 14 stress 0.1602666 
 Run 15 stress 0.143847 
 Run 16 stress 0.1562442 
 Run 17 stress 0.15341 
 Run 18 stress 0.1999476 
 Run 19 stress 0.1541285 
 Run 20 stress 0.1484817 
-Run 21 stress 0.1608378 
-Run 22 stress 0.1638227 
-Run 23 stress 0.1817737 
-Run 24 stress 0.1622664 
 *** Solution reached
 ~~~
 {: .output}
@@ -622,37 +618,33 @@ original data well.
 > > 
 > > 
 > > ~~~
-> > Run 0 stress 0.0688331 
-> > Run 1 stress 0.06958135 
+> > Run 0 stress 0.06883309 
+> > Run 1 stress 0.06958173 
 > > Run 2 stress 0.0689553 
-> > ... Procrustes: rmse 0.005872248  max resid 0.05843999 
-> > Run 3 stress 0.06958234 
-> > Run 4 stress 0.06998722 
-> > Run 5 stress 0.07180568 
-> > Run 6 stress 0.07039164 
-> > Run 7 stress 0.07085392 
+> > ... Procrustes: rmse 0.005878326  max resid 0.05848458 
+> > Run 3 stress 0.06957764 
+> > Run 4 stress 0.07000042 
+> > Run 5 stress 0.07181074 
+> > Run 6 stress 0.07033401 
+> > Run 7 stress 0.07085398 
 > > Run 8 stress 0.06895907 
-> > ... Procrustes: rmse 0.006904971  max resid 0.08102637 
+> > ... Procrustes: rmse 0.006909204  max resid 0.08103494 
 > > Run 9 stress 0.07078944 
 > > Run 10 stress 0.06956202 
-> > Run 11 stress 0.07382995 
+> > Run 11 stress 0.07379008 
 > > Run 12 stress 0.07324842 
-> > Run 13 stress 0.06962017 
+> > Run 13 stress 0.06961728 
 > > Run 14 stress 0.06889305 
-> > ... Procrustes: rmse 0.003930006  max resid 0.05685175 
+> > ... Procrustes: rmse 0.003933647  max resid 0.05689851 
 > > Run 15 stress 0.06888851 
-> > ... Procrustes: rmse 0.006876936  max resid 0.0808861 
-> > Run 16 stress 0.0688348 
-> > ... Procrustes: rmse 0.0004083019  max resid 0.002545549 
+> > ... Procrustes: rmse 0.006879761  max resid 0.08089582 
+> > Run 16 stress 0.06883488 
+> > ... Procrustes: rmse 0.0003875964  max resid 0.002401171 
 > > ... Similar to previous best
-> > Run 17 stress 0.07046705 
-> > Run 18 stress 0.06956713 
+> > Run 17 stress 0.07052512 
+> > Run 18 stress 0.06956379 
 > > Run 19 stress 0.07053079 
 > > Run 20 stress 0.07194726 
-> > Run 21 stress 0.0702962 
-> > Run 22 stress 0.07231626 
-> > Run 23 stress 0.0696101 
-> > Run 24 stress 0.06970453 
 > > *** Solution reached
 > > ~~~
 > > {: .output}
@@ -673,107 +665,106 @@ original data well.
 > > 
 > > 
 > > ~~~
-> > Run 0 stress 0.09379872 
-> > Run 1 stress 0.1026698 
+> > Run 0 stress 0.09379868 
+> > Run 1 stress 0.1026697 
 > > Run 2 stress 0.1002676 
 > > Run 3 stress 0.1023272 
 > > Run 4 stress 0.09287257 
 > > ... New best solution
-> > ... Procrustes: rmse 0.01237011  max resid 0.1707368 
+> > ... Procrustes: rmse 0.01237104  max resid 0.1707511 
 > > Run 5 stress 0.09588158 
-> > Run 6 stress 0.1093368 
-> > Run 7 stress 0.1029276 
+> > Run 6 stress 0.1093369 
+> > Run 7 stress 0.1030217 
 > > Run 8 stress 0.1034482 
 > > Run 9 stress 0.09738996 
-> > Run 10 stress 0.1082283 
-> > Run 11 stress 0.1028023 
+> > Run 10 stress 0.108229 
+> > Run 11 stress 0.1028017 
 > > Run 12 stress 0.1036501 
 > > Run 13 stress 0.09532804 
-> > Run 14 stress 0.102258 
-> > Run 15 stress 0.1024873 
-> > Run 16 stress 0.1013874 
+> > Run 14 stress 0.1022372 
+> > Run 15 stress 0.1024869 
+> > Run 16 stress 0.101386 
 > > Run 17 stress 0.09505229 
 > > Run 18 stress 0.09796259 
 > > Run 19 stress 0.1068903 
 > > Run 20 stress 0.1066879 
-> > Run 21 stress 0.1086129 
-> > Run 22 stress 0.100432 
-> > Run 23 stress 0.102715 
-> > Run 24 stress 0.1071413 
+> > Run 21 stress 0.1085169 
+> > Run 22 stress 0.1004321 
+> > Run 23 stress 0.1027152 
+> > Run 24 stress 0.1071443 
 > > Run 25 stress 0.1047762 
-> > Run 26 stress 0.09526129 
+> > Run 26 stress 0.09526087 
 > > Run 27 stress 0.09958195 
-> > Run 28 stress 0.09607154 
-> > Run 29 stress 0.1060663 
-> > Run 30 stress 0.1075293 
+> > Run 28 stress 0.09607168 
+> > Run 29 stress 0.1060682 
+> > Run 30 stress 0.1075295 
 > > Run 31 stress 0.09590724 
 > > Run 32 stress 0.09845323 
 > > Run 33 stress 0.1082491 
 > > Run 34 stress 0.09620151 
-> > Run 35 stress 0.1047376 
-> > Run 36 stress 0.09496087 
-> > Run 37 stress 0.09609119 
-> > Run 38 stress 0.1064076 
-> > Run 39 stress 0.105015 
-> > Run 40 stress 0.09626336 
+> > Run 35 stress 0.1047374 
+> > Run 36 stress 0.09495708 
+> > Run 37 stress 0.09609133 
+> > Run 38 stress 0.1064078 
+> > Run 39 stress 0.1050149 
+> > Run 40 stress 0.09626938 
 > > Run 41 stress 0.1028917 
-> > Run 42 stress 0.1019894 
+> > Run 42 stress 0.101983 
 > > Run 43 stress 0.09481307 
 > > Run 44 stress 0.09446836 
 > > Run 45 stress 0.1070549 
 > > Run 46 stress 0.09458377 
 > > Run 47 stress 0.1038932 
-> > Run 48 stress 0.09983303 
-> > Run 49 stress 0.1001508 
+> > Run 48 stress 0.09983213 
+> > Run 49 stress 0.1001502 
 > > Run 50 stress 0.09829187 
-> > Run 51 stress 0.09990176 
-> > Run 52 stress 0.1085232 
+> > Run 51 stress 0.09990189 
+> > Run 52 stress 0.1090401 
 > > Run 53 stress 0.09551422 
 > > Run 54 stress 0.0977556 
 > > Run 55 stress 0.09406389 
 > > Run 56 stress 0.1041708 
-> > Run 57 stress 0.0963039 
+> > Run 57 stress 0.09631193 
 > > Run 58 stress 0.09624402 
-> > Run 59 stress 0.09865697 
-> > Run 60 stress 0.1061679 
-> > Run 61 stress 0.1027311 
-> > Run 62 stress 0.1059518 
+> > Run 59 stress 0.09865492 
+> > Run 60 stress 0.1061676 
+> > Run 61 stress 0.1027302 
+> > Run 62 stress 0.1059547 
 > > Run 63 stress 0.1066049 
 > > Run 64 stress 0.09887407 
 > > Run 65 stress 0.09469729 
-> > Run 66 stress 0.1066662 
+> > Run 66 stress 0.106663 
 > > Run 67 stress 0.101879 
-> > Run 68 stress 0.09416585 
+> > Run 68 stress 0.094166 
 > > Run 69 stress 0.09884343 
 > > Run 70 stress 0.1046467 
 > > Run 71 stress 0.09468667 
 > > Run 72 stress 0.09958167 
-> > Run 73 stress 0.09539729 
-> > Run 74 stress 0.1070031 
+> > Run 73 stress 0.09540004 
+> > Run 74 stress 0.107003 
 > > Run 75 stress 0.09957389 
-> > Run 76 stress 0.09495955 
+> > Run 76 stress 0.09495904 
 > > Run 77 stress 0.09773001 
-> > Run 78 stress 0.106397 
+> > Run 78 stress 0.1063964 
 > > Run 79 stress 0.1037537 
 > > Run 80 stress 0.09875277 
 > > Run 81 stress 0.09479951 
-> > Run 82 stress 0.1040475 
+> > Run 82 stress 0.1040489 
 > > Run 83 stress 0.09430034 
 > > Run 84 stress 0.1064933 
 > > Run 85 stress 0.1005868 
-> > Run 86 stress 0.1061674 
+> > Run 86 stress 0.1061675 
 > > Run 87 stress 0.09729939 
-> > Run 88 stress 0.09810385 
+> > Run 88 stress 0.09810382 
 > > Run 89 stress 0.1051389 
-> > Run 90 stress 0.1032564 
+> > Run 90 stress 0.1032565 
 > > Run 91 stress 0.09523564 
 > > Run 92 stress 0.09795836 
 > > Run 93 stress 0.1012748 
 > > Run 94 stress 0.09966816 
 > > Run 95 stress 0.09287379 
 > > ... Procrustes: rmse 0.000348827  max resid 0.003927931 
 > > ... Similar to previous best
-> > Run 96 stress 0.1056731 
 > > *** Solution reached
 > > ~~~
 > > {: .output}