diff --git a/docs/articles/Cell_Bender_Functions.html b/docs/articles/Cell_Bender_Functions.html index ff6ed85e0..8a609db4b 100644 --- a/docs/articles/Cell_Bender_Functions.html +++ b/docs/articles/Cell_Bender_Functions.html @@ -130,7 +130,7 @@

Cell Bender Functionality & Plotting

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/Cell_Bender_Functions.Rmd diff --git a/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-17-1.png b/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-17-1.png index 5e6c4ddd0..1fb453799 100644 Binary files a/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-17-1.png and b/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-17-1.png differ diff --git a/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-19-1.png b/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-19-1.png index 7e7c4ebbe..5b67e3599 100644 Binary files a/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-19-1.png and b/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-19-1.png differ diff --git a/docs/articles/Color_Palettes.html b/docs/articles/Color_Palettes.html index 5df25d450..4a7874522 100644 --- a/docs/articles/Color_Palettes.html +++ b/docs/articles/Color_Palettes.html @@ -129,7 +129,7 @@

Customized Color Palettes & Themes

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/Color_Palettes.Rmd diff --git a/docs/articles/FAQ.html b/docs/articles/FAQ.html index c8a6c3024..2b34aa0c9 100644 --- a/docs/articles/FAQ.html +++ b/docs/articles/FAQ.html @@ -129,7 +129,7 @@

Frequently Asked Questions

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/FAQ.Rmd diff --git a/docs/articles/Gene_Expression_Plotting.html b/docs/articles/Gene_Expression_Plotting.html index c31711b4b..8d1b536f2 100644 --- a/docs/articles/Gene_Expression_Plotting.html +++ b/docs/articles/Gene_Expression_Plotting.html @@ -129,7 +129,7 @@

Plotting #1: Analysis Plots

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/Gene_Expression_Plotting.Rmd diff --git a/docs/articles/Helpers_and_Utilities.html b/docs/articles/Helpers_and_Utilities.html index 47b19014e..4fa583dc1 100644 --- a/docs/articles/Helpers_and_Utilities.html +++ b/docs/articles/Helpers_and_Utilities.html @@ -130,7 +130,7 @@

General Helpers & Utilities

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/Helpers_and_Utilities.Rmd @@ -550,7 +550,7 @@

Extract all meta data (cel Memory CD4 T -sample4 +sample2 Batch2 @@ -573,7 +573,7 @@

Extract all meta data (cel B -sample6 +sample5 Batch2 @@ -596,7 +596,7 @@

Extract all meta data (cel Memory CD4 T -sample2 +sample5 Batch1 @@ -622,7 +622,7 @@

Extract all meta data (cel sample6 -Batch2 +Batch1 @@ -642,10 +642,10 @@

Extract all meta data (cel NK -sample4 +sample5 -Batch2 +Batch1 @@ -665,10 +665,10 @@

Extract all meta data (cel Memory CD4 T -sample4 +sample3 -Batch1 +Batch2 @@ -688,10 +688,10 @@

Extract all meta data (cel CD8 T -sample1 +sample4 -Batch1 +Batch2 @@ -711,7 +711,7 @@

Extract all meta data (cel CD8 T -sample3 +sample5 Batch1 @@ -734,10 +734,10 @@

Extract all meta data (cel Naive CD4 T -sample4 +sample1 -Batch2 +Batch1 @@ -757,7 +757,7 @@

Extract all meta data (cel FCGR3A+ Mono -sample2 +sample1 Batch2 @@ -800,7 +800,7 @@

Extract sample-level meta da pbmc3k -CD8 T +Naive CD4 T sample1 @@ -823,7 +823,7 @@

Extract sample-level meta da sample2 -Batch1 +Batch2 @@ -834,13 +834,13 @@

Extract sample-level meta da pbmc3k -CD8 T +Memory CD4 T sample3 -Batch1 +Batch2 @@ -851,7 +851,7 @@

Extract sample-level meta da pbmc3k -Memory CD4 T +CD8 T sample4 @@ -868,13 +868,13 @@

Extract sample-level meta da pbmc3k -Memory CD4 T +B sample5 -Batch1 +Batch2 @@ -885,13 +885,13 @@

Extract sample-level meta da pbmc3k -B +CD14+ Mono sample6 -Batch2 +Batch1 @@ -939,7 +939,7 @@

Remove columns tha sample2 -Batch1 +Batch2 @@ -950,7 +950,7 @@
Remove columns tha sample3 -Batch1 +Batch2 @@ -972,7 +972,7 @@
Remove columns tha sample5 -Batch1 +Batch2 @@ -983,7 +983,7 @@
Remove columns tha sample6 -Batch2 +Batch1 @@ -1032,10 +1032,10 @@
Merge with sample-level Batch1 -2284.5 +2189.0 -841 +816.0 @@ -1046,13 +1046,13 @@
Merge with sample-level sample2 -Batch1 +Batch2 -2143.0 +2194.0 -793 +814.0 @@ -1063,13 +1063,13 @@
Merge with sample-level sample3 -Batch1 +Batch2 -2194.0 +2209.0 -816 +817.0 @@ -1083,10 +1083,10 @@
Merge with sample-level Batch2 -2256.0 +2258.5 -819 +823.0 @@ -1097,13 +1097,13 @@
Merge with sample-level sample5 -Batch1 +Batch2 -2157.0 +2174.5 -816 +813.5 @@ -1114,13 +1114,13 @@
Merge with sample-level sample6 -Batch2 +Batch1 -2212.0 +2163.0 -813 +810.0 @@ -1137,7 +1137,7 @@
Merge with sample-level 2196.0 -816 +816.0 diff --git a/docs/articles/Installation.html b/docs/articles/Installation.html index 88ae77c13..25f26d105 100644 --- a/docs/articles/Installation.html +++ b/docs/articles/Installation.html @@ -129,7 +129,7 @@

Installation Instructions for scCustomize

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/Installation.Rmd diff --git a/docs/articles/Iterative_Plotting.html b/docs/articles/Iterative_Plotting.html index 8cfbf13d3..29e4b3d81 100644 --- a/docs/articles/Iterative_Plotting.html +++ b/docs/articles/Iterative_Plotting.html @@ -129,7 +129,7 @@

Plotting #4: Iterative Plotting Functions

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/Iterative_Plotting.Rmd diff --git a/docs/articles/LIGER_Functions.html b/docs/articles/LIGER_Functions.html index 22534e8f5..877c74809 100644 --- a/docs/articles/LIGER_Functions.html +++ b/docs/articles/LIGER_Functions.html @@ -129,7 +129,7 @@

LIGER Plotting & Functionality

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/LIGER_Functions.Rmd diff --git a/docs/articles/Markers_and_Cluster_Annotation.html b/docs/articles/Markers_and_Cluster_Annotation.html index c67bfb591..c1e20ba6a 100644 --- a/docs/articles/Markers_and_Cluster_Annotation.html +++ b/docs/articles/Markers_and_Cluster_Annotation.html @@ -131,7 +131,7 @@

Marker Identification & Cluster Annotation Helpers

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/Markers_and_Cluster_Annotation.Rmd diff --git a/docs/articles/Misc_Functions.html b/docs/articles/Misc_Functions.html index d7aec8c2a..a1aa83940 100644 --- a/docs/articles/Misc_Functions.html +++ b/docs/articles/Misc_Functions.html @@ -129,7 +129,7 @@

Misc Functions

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/Misc_Functions.Rmd diff --git a/docs/articles/QC_Plots.html b/docs/articles/QC_Plots.html index 76799dc11..39a8e759f 100644 --- a/docs/articles/QC_Plots.html +++ b/docs/articles/QC_Plots.html @@ -130,7 +130,7 @@

Plotting #2: QC Plots

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/QC_Plots.Rmd diff --git a/docs/articles/Read_and_Write_Functions.html b/docs/articles/Read_and_Write_Functions.html index 44803ac83..416f9da3b 100644 --- a/docs/articles/Read_and_Write_Functions.html +++ b/docs/articles/Read_and_Write_Functions.html @@ -129,7 +129,7 @@

Read & Write Data Functions

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/Read_and_Write_Functions.Rmd diff --git a/docs/articles/Sequencing_QC_Plots.html b/docs/articles/Sequencing_QC_Plots.html index 3940d8872..b22641a8d 100644 --- a/docs/articles/Sequencing_QC_Plots.html +++ b/docs/articles/Sequencing_QC_Plots.html @@ -130,7 +130,7 @@

Plotting #3: Sequencing QC Plots/Analysis

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/Sequencing_QC_Plots.Rmd diff --git a/docs/articles/Statistics.html b/docs/articles/Statistics.html index b4cf53405..d14166942 100644 --- a/docs/articles/Statistics.html +++ b/docs/articles/Statistics.html @@ -130,7 +130,7 @@

Statistics Functions

-

Compiled: November 13, +

Compiled: November 15, 2023

Source: vignettes/articles/Statistics.Rmd @@ -235,28 +235,28 @@

Cells Per Identity -168 +182 -176 +180 -161 +157 -192 +178 -26.6666667 +27.5757576 -25.1788269 +27.5229358 -24.845679 +23.4328358 -29.0468986 +27.217125 @@ -270,28 +270,28 @@

Cells Per Identity -106 +120 -134 +114 -113 +135 -130 +114 -16.8253968 +18.1818182 -19.1702432 +17.4311927 -17.438272 +20.1492537 -19.6671710 +17.431193 @@ -308,25 +308,25 @@

Cells Per Identity -138 +126 -116 +121 -118 +125 -17.1428571 +16.3636364 -19.7424893 +19.2660550 -17.901235 +18.0597015 -17.8517398 +19.113150 @@ -340,28 +340,28 @@

Cells Per Identity -81 +97 -80 +93 -100 +79 -83 +75 -12.8571429 +14.6969697 -11.4449213 +14.2201835 -15.432099 +11.7910448 -12.5567322 +11.467890 @@ -375,28 +375,28 @@

Cells Per Identity -76 +66 -75 +52 -64 +82 -56 +71 -12.0634921 +10.0000000 -10.7296137 +7.9510703 -9.876543 +12.2388060 -8.4720121 +10.856269 @@ -410,28 +410,28 @@

Cells Per Identity -45 +46 -37 +45 -44 +35 36 -7.1428571 +6.9696970 -5.2932761 +6.8807339 -6.790123 +5.2238806 -5.4462935 +5.504587 @@ -445,28 +445,28 @@

Cells Per Identity -35 +32 -48 +31 -41 +52 -31 +40 -5.5555556 +4.8484848 -6.8669528 +4.7400612 -6.327160 +7.7611940 -4.6898638 +6.116208 @@ -480,10 +480,10 @@

Cells Per Identity -8 +5 -7 +10 7 @@ -492,16 +492,16 @@

Cells Per Identity -1.2698413 +0.7575758 -1.0014306 +1.5290520 -1.080247 +1.0447761 -1.5128593 +1.529052 @@ -515,10 +515,10 @@

Cells Per Identity -3 +4 -4 +3 2 @@ -527,16 +527,16 @@

Cells Per Identity -0.4761905 +0.6060606 -0.5722461 +0.4587156 -0.308642 +0.2985075 -0.7564297 +0.764526 @@ -550,16 +550,16 @@

Cells Per Identity -630 +660 -699 +654 -648 +670 -661 +654 100.0000000 @@ -568,10 +568,10 @@

Cells Per Identity -100.000000 +100.0000000 -100.0000000 +100.000000 @@ -619,16 +619,16 @@

Cells Per Identity -329 +339 -368 +358 -25.7433490 +25.4887218 -27.0588235 +27.3700306 @@ -642,16 +642,16 @@

Cells Per Identity -219 +255 -264 +228 -17.1361502 +19.1729323 -19.4117647 +17.4311927 @@ -665,16 +665,16 @@

Cells Per Identity -224 +229 -256 +251 -17.5273865 +17.2180451 -18.8235294 +19.1896024 @@ -688,16 +688,16 @@

Cells Per Identity -181 +176 -163 +168 -14.1627543 +13.2330827 -11.9852941 +12.8440367 @@ -711,16 +711,16 @@

Cells Per Identity -140 +148 -131 +123 -10.9546166 +11.1278195 -9.6323529 +9.4036697 @@ -734,16 +734,16 @@

Cells Per Identity -89 +81 -73 +81 -6.9640063 +6.0902256 -5.3676471 +6.1926606 @@ -757,16 +757,16 @@

Cells Per Identity -76 +84 -79 +71 -5.9467919 +6.3157895 -5.8088235 +5.4281346 @@ -780,16 +780,16 @@

Cells Per Identity -15 +12 -17 +20 -1.1737089 +0.9022556 -1.2500000 +1.5290520 @@ -803,16 +803,16 @@

Cells Per Identity -5 +6 -9 +8 -0.3912363 +0.4511278 -0.6617647 +0.6116208 @@ -826,10 +826,10 @@

Cells Per Identity -1278 +1330 -1360 +1308 100.0000000 @@ -962,9 +962,6 @@

Change grouping variable -sample3 - - sample2 @@ -973,6 +970,9 @@

Change grouping variable sample1 + +sample3 + @@ -980,16 +980,16 @@

Change grouping variable -11.11111 +12.99694 -11.87411 +10.24465 -11.95159 +12.27273 -11.90476 +11.34328 @@ -997,16 +997,16 @@

Change grouping variable -10.49383 +12.84404 -13.16166 +10.85627 -12.40545 +10.90909 -10.95238 +12.53731 @@ -1024,10 +1024,10 @@

Split within groups -Naive.CD4.T_Group.1 +Naive.CD4.T_Group.2 -Naive.CD4.T_Group.2 +Naive.CD4.T_Group.1 Memory.CD4.T_Group.2 @@ -1066,17 +1066,17 @@

Split within groups -DC_Group.1 - - DC_Group.2 -Platelet_Group.2 +DC_Group.1 Platelet_Group.1 + +Platelet_Group.2 + @@ -1084,52 +1084,52 @@

Split within groups -6.382979 +6.424581 -7.065217 +7.079646 -15.909091 +15.789474 -15.981735 +16.078431 -23.04688 +23.505976 -25.892857 +25.327511 -1.657459 +2.272727 -1.226994 +0.5952381 -3.571429 +2.702703 -1.526718 +2.439024 -25.842697 +27.160494 -28.767123 +27.16049 -1.265823 +0.000000 -0.00000 +1.190476 -13.33333 +40 -52.941176 +25 0 @@ -1143,52 +1143,52 @@

Split within groups -11.854103 +15.083799 -14.673913 +11.504425 -9.090909 +9.210526 -8.675799 +8.627451 -2.34375 +2.390438 -1.339286 +1.310044 -3.314917 +1.704546 -1.840491 +3.5714286 -42.142857 +54.729730 -59.541985 +45.528455 -3.370786 +1.234568 -4.109589 +6.17284 -6.329114 +8.450704 -10.52632 +8.333333 -0.00000 +5 -5.882353 +0 0 @@ -1352,19 +1352,19 @@

Basic Use -2175.5 +2210.0 -820.5 +804 -2.062129 +1.981326 -36.51243 +37.63146 -38.72930 +39.75322 @@ -1372,19 +1372,19 @@

Basic Use -2237.0 +2188.5 -820.0 +818 -2.005975 +2.015371 -36.31425 +37.32674 -38.63042 +39.33562 @@ -1392,19 +1392,19 @@

Basic Use -2255.5 +2224.5 -828.5 +829 -2.025659 +2.056494 -37.03454 +36.19158 -39.09636 +38.33063 @@ -1412,19 +1412,19 @@

Basic Use -2189.0 +2216.5 -806.0 +820 -1.960784 +1.982013 -37.43363 +36.81153 -39.74237 +38.96528 @@ -1435,7 +1435,7 @@

Basic Use -819.0 +819 2.010702 @@ -1489,22 +1489,22 @@

Additional Variables -2175.5 +2210.0 -820.5 +804 -2.062129 +1.981326 -36.51243 +37.63146 -38.72930 +39.75322 --0.0918005 +-0.1808143 @@ -1512,22 +1512,22 @@

Additional Variables -2237.0 +2188.5 -820.0 +818 -2.005975 +2.015371 -36.31425 +37.32674 -38.63042 +39.33562 --0.0646868 +-0.0791349 @@ -1535,22 +1535,22 @@

Additional Variables -2255.5 +2224.5 -828.5 +829 -2.025659 +2.056494 -37.03454 +36.19158 -39.09636 +38.33063 --0.1521147 +-0.0584612 @@ -1558,22 +1558,22 @@

Additional Variables -2189.0 +2216.5 -806.0 +820 -1.960784 +1.982013 -37.43363 +36.81153 -39.74237 +38.96528 --0.0593373 +-0.0827705 @@ -1584,7 +1584,7 @@

Additional Variables -819.0 +819 2.010702 @@ -1638,19 +1638,19 @@

Calculate Median Absolute Deviatio sample1 -703.4937 +738.3348 -186.0663 +196.4445 -0.7930814 +0.7893466 -12.21083 +11.90301 -11.91618 +11.68093 @@ -1658,19 +1658,19 @@

Calculate Median Absolute Deviatio sample2 -782.8128 +782.0715 -194.2206 +204.5988 -0.7781392 +0.7605386 -12.54379 +11.32629 -12.56013 +10.95702 @@ -1678,19 +1678,19 @@

Calculate Median Absolute Deviatio sample3 -719.0610 +631.5876 -182.3598 +177.1707 -0.7518263 +0.7790401 -11.42940 +11.81377 -11.52044 +11.56751 @@ -1698,19 +1698,19 @@

Calculate Median Absolute Deviatio sample4 -664.2048 +730.9218 -188.2902 +184.5837 -0.7614907 +0.7421755 -11.14546 +12.08440 -10.82339 +11.80106 diff --git a/docs/articles/Statistics_files/figure-html/unnamed-chunk-22-1.png b/docs/articles/Statistics_files/figure-html/unnamed-chunk-22-1.png index fd95c3c44..dfc001658 100644 Binary files a/docs/articles/Statistics_files/figure-html/unnamed-chunk-22-1.png and b/docs/articles/Statistics_files/figure-html/unnamed-chunk-22-1.png differ diff --git a/docs/news/index.html b/docs/news/index.html index c5f32b627..c5e9af883 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -105,7 +105,7 @@

Changelog

-

scCustomize 2.0.0 (2023-11-13)

+

scCustomize 2.0.0 (2023-11-13)2023-11-14

Added

  • Added support for metrics produced by Cell Ranger multi pipeline to Read10X_Metrics via new parameter cellranger_multi.
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index ba94d8215..903e5817b 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -16,7 +16,7 @@ articles: Read_and_Write_Functions: Read_and_Write_Functions.html Sequencing_QC_Plots: Sequencing_QC_Plots.html Statistics: Statistics.html -last_built: 2023-11-14T00:36Z +last_built: 2023-11-15T19:21Z urls: reference: https://samuel-marsh.github.io/scCustomize/reference article: https://samuel-marsh.github.io/scCustomize/articles diff --git a/docs/reference/Blank_Theme-1.png b/docs/reference/Blank_Theme-1.png index c545d4dc5..bb7348bb4 100644 Binary files a/docs/reference/Blank_Theme-1.png and b/docs/reference/Blank_Theme-1.png differ diff --git a/inst/pkgdown.yml b/inst/pkgdown.yml index ba94d8215..903e5817b 100644 --- a/inst/pkgdown.yml +++ b/inst/pkgdown.yml @@ -16,7 +16,7 @@ articles: Read_and_Write_Functions: Read_and_Write_Functions.html Sequencing_QC_Plots: Sequencing_QC_Plots.html Statistics: Statistics.html -last_built: 2023-11-14T00:36Z +last_built: 2023-11-15T19:21Z urls: reference: https://samuel-marsh.github.io/scCustomize/reference article: https://samuel-marsh.github.io/scCustomize/articles