From 2c5076994a5cc1d972101497726b7b0bd554aaaa Mon Sep 17 00:00:00 2001 From: Mwoo-usyd <106008614+Mwoo-usyd@users.noreply.github.com> Date: Fri, 16 Aug 2024 06:59:33 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20SydneyBi?= =?UTF-8?q?oX/wSIR@8abdcb5c151e1255cd699db12800f7665ac83905=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/wSIR_vignette.html | 113 ++++-------------- .../figure-html/unnamed-chunk-4-1.png | Bin 52357 -> 54242 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 41208 -> 40015 bytes .../figure-html/unnamed-chunk-6-2.png | Bin 69984 -> 68637 bytes .../figure-html/unnamed-chunk-7-1.png | Bin 493686 -> 521388 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 281720 -> 318415 bytes pkgdown.yml | 2 +- reference/exploreWSIRParams-1.png | Bin 52164 -> 53857 bytes reference/exploreWSIRParams.html | 2 +- search.json | 2 +- 10 files changed, 28 insertions(+), 91 deletions(-) diff --git a/articles/wSIR_vignette.html b/articles/wSIR_vignette.html index 7fc0351..f7c21ea 100644 --- a/articles/wSIR_vignette.html +++ b/articles/wSIR_vignette.html @@ -407,95 +407,32 @@
dim(sample2_low_dim_exprs)
## [1] 2986 50
+## [1] 2986 11
Observe some of sample 2’s low-dimensional gene expression data:
head(sample2_low_dim_exprs)
## 6 x 50 Matrix of class "dgeMatrix"
-## [,1] [,2] [,3] [,4] [,5]
-## embryo2_Pos29_cell103_z2 0.4033853 1.1406906 0.9342274 -0.6690855 -1.183150
-## embryo2_Pos29_cell11_z2 -0.3976906 1.1332231 0.2099434 -0.9262752 -1.452108
-## embryo2_Pos29_cell110_z2 2.8521104 -0.5786873 1.7263464 -0.4939740 -1.545942
-## embryo2_Pos29_cell123_z2 3.0851403 -0.8251517 0.6092021 -0.5964077 -1.349482
-## embryo2_Pos29_cell128_z2 1.7075150 1.5915042 -0.4335929 -0.6712088 -1.829439
-## embryo2_Pos29_cell129_z2 1.5921375 1.3481260 -0.4065247 0.1631131 -1.854096
-## [,6] [,7] [,8] [,9]
-## embryo2_Pos29_cell103_z2 -0.4204610 1.6947454 1.2416277 1.59455858
-## embryo2_Pos29_cell11_z2 -0.3434242 -0.2826430 0.9156203 -0.01792227
-## embryo2_Pos29_cell110_z2 1.9442965 0.9077402 1.1414361 0.88014085
-## embryo2_Pos29_cell123_z2 1.1061599 0.8913565 1.5925948 0.98843793
-## embryo2_Pos29_cell128_z2 1.3707372 -0.8978932 1.5563948 -0.37715216
-## embryo2_Pos29_cell129_z2 0.2094885 -0.5237807 1.1472571 -0.85171920
-## [,10] [,11] [,12] [,13]
-## embryo2_Pos29_cell103_z2 0.87866970 0.1545180 0.1226031 -0.007213118
-## embryo2_Pos29_cell11_z2 0.17127514 -0.6272048 -0.3600095 -0.041998794
-## embryo2_Pos29_cell110_z2 0.10466509 -1.1003643 -0.2268346 -0.104254143
-## embryo2_Pos29_cell123_z2 0.55220381 -0.9919387 -1.0468458 -0.535745625
-## embryo2_Pos29_cell128_z2 -0.29244180 -0.4787738 -0.4219472 0.599094022
-## embryo2_Pos29_cell129_z2 0.06985137 -0.5388220 0.4363146 1.735954576
-## [,14] [,15] [,16] [,17]
-## embryo2_Pos29_cell103_z2 -0.26403842 -0.1667892 -0.1674317 -0.84025812
-## embryo2_Pos29_cell11_z2 0.02027922 -0.1912650 0.4971098 -0.03229449
-## embryo2_Pos29_cell110_z2 -1.07366605 -0.6264570 1.6476511 -1.85407880
-## embryo2_Pos29_cell123_z2 -0.26912731 0.1633992 1.3475923 -1.08817836
-## embryo2_Pos29_cell128_z2 -0.11342803 -0.7663365 0.3608360 1.22403405
-## embryo2_Pos29_cell129_z2 0.66379966 -1.2086104 -0.1218102 0.83435792
-## [,18] [,19] [,20] [,21]
-## embryo2_Pos29_cell103_z2 -1.2032348 1.923318769 1.3525301 -0.90228595
-## embryo2_Pos29_cell11_z2 -0.6919699 0.005947897 0.8091922 -2.27363291
-## embryo2_Pos29_cell110_z2 -1.2730726 0.277065604 -0.5378237 -0.03316571
-## embryo2_Pos29_cell123_z2 -0.8927717 -0.104622662 0.3044058 0.39915731
-## embryo2_Pos29_cell128_z2 -0.8265268 -1.261045070 0.1299859 -1.53565884
-## embryo2_Pos29_cell129_z2 -1.8961773 -1.151805215 0.6253794 -0.99818155
-## [,22] [,23] [,24] [,25]
-## embryo2_Pos29_cell103_z2 0.21986234 1.7140137 1.7309975 0.74602409
-## embryo2_Pos29_cell11_z2 0.20854077 -0.1540283 -1.1164174 -0.05310395
-## embryo2_Pos29_cell110_z2 -0.27216629 -0.5039993 -0.1865994 -0.79026591
-## embryo2_Pos29_cell123_z2 -0.54615606 -1.0883485 -0.6943658 -1.00291231
-## embryo2_Pos29_cell128_z2 0.03956295 -0.5873782 0.1000467 -1.63964609
-## embryo2_Pos29_cell129_z2 0.14399058 -0.4114348 -0.3822816 -0.54459743
-## [,26] [,27] [,28] [,29] [,30]
-## embryo2_Pos29_cell103_z2 0.35040014 1.9244114 1.0994142 0.8017454 0.06630328
-## embryo2_Pos29_cell11_z2 -0.04033414 2.4342194 0.1775621 -0.4003911 1.99938051
-## embryo2_Pos29_cell110_z2 -0.16474872 1.2637777 0.1026267 -0.2428714 0.58283064
-## embryo2_Pos29_cell123_z2 -0.32528226 0.6078707 -0.1877018 -0.3551147 0.25573785
-## embryo2_Pos29_cell128_z2 -1.00529104 1.7031747 1.2513900 -0.4557731 0.18030373
-## embryo2_Pos29_cell129_z2 -1.13653850 1.8444441 -0.1379572 -0.2130001 0.62098951
-## [,31] [,32] [,33] [,34]
-## embryo2_Pos29_cell103_z2 0.018409306 0.3581564 0.29453308 -1.22243261
-## embryo2_Pos29_cell11_z2 -0.001305528 -0.2014190 0.32778650 -0.54913966
-## embryo2_Pos29_cell110_z2 0.195284812 -0.3263791 0.32772422 0.19305454
-## embryo2_Pos29_cell123_z2 -0.906437879 -0.5392833 0.06349666 -0.32993882
-## embryo2_Pos29_cell128_z2 0.863123205 -0.2326273 0.49177219 -0.22691262
-## embryo2_Pos29_cell129_z2 0.555737550 0.5669336 0.12087072 0.00246478
-## [,35] [,36] [,37] [,38]
-## embryo2_Pos29_cell103_z2 -0.83359997 -0.5626265 0.27147656 0.7485256
-## embryo2_Pos29_cell11_z2 -1.38506568 0.2047991 -0.55698357 -0.7616677
-## embryo2_Pos29_cell110_z2 -0.01615896 -0.1681945 -0.03517469 -0.2185019
-## embryo2_Pos29_cell123_z2 -1.26199626 -0.3987478 0.47164230 -0.1381785
-## embryo2_Pos29_cell128_z2 -1.14278654 -1.1506724 0.50078317 -0.3879110
-## embryo2_Pos29_cell129_z2 -0.45564116 -0.2931448 0.29778589 -0.6482173
-## [,39] [,40] [,41] [,42]
-## embryo2_Pos29_cell103_z2 0.41777984 0.4383434 -2.50295425 0.3573508
-## embryo2_Pos29_cell11_z2 0.77111513 -1.1546844 -0.50097650 0.6704736
-## embryo2_Pos29_cell110_z2 0.16336572 -0.3048052 -0.92621527 0.7283678
-## embryo2_Pos29_cell123_z2 -0.05387757 -0.4122033 -0.09306071 0.7372195
-## embryo2_Pos29_cell128_z2 0.19807621 -0.5889438 -0.69818005 0.6589139
-## embryo2_Pos29_cell129_z2 0.20978183 -1.0426766 -1.42117800 0.4702585
-## [,43] [,44] [,45] [,46]
-## embryo2_Pos29_cell103_z2 -1.6484713 -0.4895815 -0.59446975 0.71408399
-## embryo2_Pos29_cell11_z2 0.9528671 -0.2195819 0.62827717 -0.52972392
-## embryo2_Pos29_cell110_z2 0.2140502 0.2567104 -0.48469833 0.12967940
-## embryo2_Pos29_cell123_z2 -0.0273528 0.1112703 0.02530738 -0.21172745
-## embryo2_Pos29_cell128_z2 0.4508320 0.2628886 0.19487445 -0.07063846
-## embryo2_Pos29_cell129_z2 0.2349036 0.9833049 -0.10346168 0.52593553
-## [,47] [,48] [,49] [,50]
-## embryo2_Pos29_cell103_z2 1.23068370 -0.3799625 0.3894140 0.39796516
-## embryo2_Pos29_cell11_z2 -1.08694513 -0.5879184 2.0141168 0.02853424
-## embryo2_Pos29_cell110_z2 -0.37968571 -0.4806475 0.5887303 0.06295446
-## embryo2_Pos29_cell123_z2 -0.99822491 -0.5224671 0.6332211 -0.44533316
-## embryo2_Pos29_cell128_z2 0.59261012 0.2320150 0.7073504 0.25872334
-## embryo2_Pos29_cell129_z2 -0.01375025 -0.1666974 0.5304861 0.23373365
+## 6 x 11 Matrix of class "dgeMatrix"
+## [,1] [,2] [,3] [,4]
+## embryo2_Pos29_cell103_z2 1.0203749 0.3367455 -1.3565745 2.011629895
+## embryo2_Pos29_cell11_z2 0.8550455 -0.1381868 0.6183848 0.919536065
+## embryo2_Pos29_cell110_z2 1.3131534 1.1042273 -1.1648193 0.022762202
+## embryo2_Pos29_cell123_z2 1.7482077 0.6172796 -0.7380985 -0.085068178
+## embryo2_Pos29_cell128_z2 2.3064166 1.1336468 0.4710416 0.206734258
+## embryo2_Pos29_cell129_z2 1.5117116 1.6014683 1.2877220 -0.003450743
+## [,5] [,6] [,7] [,8]
+## embryo2_Pos29_cell103_z2 0.61390285 1.55456648 -2.516180 -0.8921272
+## embryo2_Pos29_cell11_z2 -0.07641813 -0.59818316 -1.773504 0.2705088
+## embryo2_Pos29_cell110_z2 0.98520475 -0.23702497 -2.361843 -0.2183407
+## embryo2_Pos29_cell123_z2 -0.08182993 -0.25701176 -2.611020 0.2165018
+## embryo2_Pos29_cell128_z2 -0.61269069 -0.81784047 -1.366283 0.4641900
+## embryo2_Pos29_cell129_z2 -1.02771287 0.08312281 -1.672021 0.4953510
+## [,9] [,10] [,11]
+## embryo2_Pos29_cell103_z2 -0.4386751 0.31450523 -0.11242577
+## embryo2_Pos29_cell11_z2 0.8749550 0.43010169 -0.01598857
+## embryo2_Pos29_cell110_z2 -0.1858788 -0.54826197 1.65810018
+## embryo2_Pos29_cell123_z2 -0.3540539 -1.00423449 0.78208477
+## embryo2_Pos29_cell128_z2 0.8305872 -0.05368451 1.59646456
+## embryo2_Pos29_cell129_z2 -0.2054220 1.14108839 1.35546275
This low-dimensional gene expression data can then be used for any later tasks which would benefit from a low-dimensional embedding of the gene expression data for all the samples, rather than just the gene @@ -524,7 +461,7 @@
## [1] 4607 50
+## [1] 4607 7
This low-dimensional matrix can then be used for downstream tasks which would benefit from a low-dimensional embedding of sample 3’s gene expression matrix that contains information about each cell’s location. @@ -545,7 +482,7 @@
## [1] Presomitic mesoderm Presomitic mesoderm Presomitic mesoderm
-## [4] Presomitic mesoderm Presomitic mesoderm Presomitic mesoderm
+## [4] Spinal cord Spinal cord Low quality
## 24 Levels: Allantois Anterior somitic tissues ... Surface ectoderm
In the above code, we use the wSIR scores as input for a simple
KNN-based cell type classification tool. We print the tail of the
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