diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png index 67a5d5f4..9e59f9e0 100644 Binary files a/apple-touch-icon-120x120.png and b/apple-touch-icon-120x120.png differ diff --git a/apple-touch-icon-152x152.png b/apple-touch-icon-152x152.png index 152c3ced..03e8ed3d 100644 Binary files a/apple-touch-icon-152x152.png and b/apple-touch-icon-152x152.png differ diff --git a/apple-touch-icon-180x180.png b/apple-touch-icon-180x180.png index e33249d3..785839f2 100644 Binary files a/apple-touch-icon-180x180.png and b/apple-touch-icon-180x180.png differ diff --git a/apple-touch-icon-60x60.png b/apple-touch-icon-60x60.png index 6b72d42d..31a20636 100644 Binary files a/apple-touch-icon-60x60.png and b/apple-touch-icon-60x60.png differ diff --git a/apple-touch-icon-76x76.png b/apple-touch-icon-76x76.png index c53d6c42..e33185ee 100644 Binary files a/apple-touch-icon-76x76.png and b/apple-touch-icon-76x76.png differ diff --git a/apple-touch-icon.png b/apple-touch-icon.png index 1ba04501..775ed914 100644 Binary files a/apple-touch-icon.png and b/apple-touch-icon.png differ diff --git a/favicon-16x16.png b/favicon-16x16.png index d85481fb..29134f44 100644 Binary files a/favicon-16x16.png and b/favicon-16x16.png differ diff --git a/favicon-32x32.png b/favicon-32x32.png index 8909724f..b1796375 100644 Binary files a/favicon-32x32.png and b/favicon-32x32.png differ diff --git a/index.html b/index.html index 9b1ff09e..4e337b93 100644 --- a/index.html +++ b/index.html @@ -531,18 +531,18 @@

Reduce dimensions pivot_sample() |> select(contains("tSNE"), everything()) 
## [90m# A tibble: 251 × 4[39m
-##       tSNE1   tSNE2 .sample                      Call 
-##       [3m[90m<dbl>[39m[23m   [3m[90m<dbl>[39m[23m [3m[90m<chr>[39m[23m                        [3m[90m<fct>[39m[23m
-## [90m 1[39m  10.3      1.72  TCGA-A1-A0SD-01A-11R-A115-07 LumA 
-## [90m 2[39m  -[31m3[39m[31m.[39m[31m88[39m   -[31m11[39m[31m.[39m[31m0[39m   TCGA-A1-A0SF-01A-11R-A144-07 LumA 
-## [90m 3[39m  15.5     -[31m0[39m[31m.[39m[31m202[39m TCGA-A1-A0SG-01A-11R-A144-07 LumA 
-## [90m 4[39m  -[31m0[39m[31m.[39m[31m0[39m[31m81[4m3[24m[39m   3.89  TCGA-A1-A0SH-01A-11R-A084-07 LumA 
-## [90m 5[39m  -[31m5[39m[31m.[39m[31m71[39m    12.9   TCGA-A1-A0SI-01A-11R-A144-07 LumB 
-## [90m 6[39m  12.9      0.912 TCGA-A1-A0SJ-01A-11R-A084-07 LumA 
-## [90m 7[39m -[31m33[39m[31m.[39m[31m9[39m     -[31m6[39m[31m.[39m[31m38[39m  TCGA-A1-A0SK-01A-12R-A084-07 Basal
-## [90m 8[39m  -[31m7[39m[31m.[39m[31m0[39m[31m2[39m     8.48  TCGA-A1-A0SM-01A-11R-A084-07 LumA 
-## [90m 9[39m  -[31m5[39m[31m.[39m[31m68[39m     8.90  TCGA-A1-A0SN-01A-11R-A144-07 LumB 
-## [90m10[39m  23.3      2.55  TCGA-A1-A0SQ-01A-21R-A144-07 LumA 
+##     tSNE1   tSNE2 .sample                      Call 
+##     [3m[90m<dbl>[39m[23m   [3m[90m<dbl>[39m[23m [3m[90m<chr>[39m[23m                        [3m[90m<fct>[39m[23m
+## [90m 1[39m -[31m12[39m[31m.[39m[31m7[39m    0.987 TCGA-A1-A0SD-01A-11R-A115-07 LumA 
+## [90m 2[39m   4.36   6.17  TCGA-A1-A0SF-01A-11R-A144-07 LumA 
+## [90m 3[39m -[31m17[39m[31m.[39m[31m0[39m    2.40  TCGA-A1-A0SG-01A-11R-A144-07 LumA 
+## [90m 4[39m  -[31m5[39m[31m.[39m[31m84[39m   5.08  TCGA-A1-A0SH-01A-11R-A084-07 LumA 
+## [90m 5[39m  -[31m9[39m[31m.[39m[31m39[39m   4.68  TCGA-A1-A0SI-01A-11R-A144-07 LumB 
+## [90m 6[39m   5.81  -[31m2[39m[31m.[39m[31m71[39m  TCGA-A1-A0SJ-01A-11R-A084-07 LumA 
+## [90m 7[39m  32.1    9.09  TCGA-A1-A0SK-01A-12R-A084-07 Basal
+## [90m 8[39m   4.47  -[31m9[39m[31m.[39m[31m44[39m  TCGA-A1-A0SM-01A-11R-A084-07 LumA 
+## [90m 9[39m   4.95 -[31m10[39m[31m.[39m[31m9[39m   TCGA-A1-A0SN-01A-11R-A144-07 LumB 
+## [90m10[39m -[31m25[39m[31m.[39m[31m6[39m   -[31m3[39m[31m.[39m[31m70[39m  TCGA-A1-A0SQ-01A-21R-A144-07 LumA 
 ## [90m# ℹ 241 more rows[39m
 counts_SE.norm.tSNE |>
@@ -788,16 +788,16 @@ 
Test differential cell-type abund
 
## [90m# A tibble: 22 × 6[39m
 ##    .cell_type         cell_type_proportions estimate std.error statistic p.value
 ##    [3m[90m<chr>[39m[23m              [3m[90m<list>[39m[23m                   [3m[90m<dbl>[39m[23m     [3m[90m<dbl>[39m[23m     [3m[90m<dbl>[39m[23m   [3m[90m<dbl>[39m[23m
-## [90m 1[39m cibersort.B.cells… [90m<tibble [48 × 9]>[39m       0.125      0.686    0.182   0.855 
-## [90m 2[39m cibersort.B.cells… [90m<tibble [48 × 9]>[39m      -[31m0[39m[31m.[39m[31m213[39m      0.452   -[31m0[39m[31m.[39m[31m472[39m   0.637 
-## [90m 3[39m cibersort.Plasma.… [90m<tibble [48 × 9]>[39m       1.13       0.899    1.26    0.209 
-## [90m 4[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m       1.43       0.959    1.49    0.136 
-## [90m 5[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      -[31m0[39m[31m.[39m[31m757[39m      0.464   -[31m1[39m[31m.[39m[31m63[39m    0.103 
-## [90m 6[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      -[31m0[39m[31m.[39m[31m412[39m      0.328   -[31m1[39m[31m.[39m[31m26[39m    0.209 
-## [90m 7[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      -[31m1[39m[31m.[39m[31m81[39m       0.891   -[31m2[39m[31m.[39m[31m0[39m[31m3[39m    0.042[4m0[24m
-## [90m 8[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m       0.054[4m6[24m     0.632    0.086[4m5[24m  0.931 
-## [90m 9[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m       0.554      0.447    1.24    0.216 
-## [90m10[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m       0.691      0.491    1.41    0.159 
+## [90m 1[39m cibersort.B.cells… [90m<tibble [48 × 9]>[39m     -[31m2[39m[31m.[39m[31m24[39m        0.791   -[31m2[39m[31m.[39m[31m83[39m   0.004[4m6[24m[4m4[24m
+## [90m 2[39m cibersort.B.cells… [90m<tibble [48 × 9]>[39m     -[31m0[39m[31m.[39m[31m803[39m       0.430   -[31m1[39m[31m.[39m[31m87[39m   0.061[4m9[24m 
+## [90m 3[39m cibersort.Plasma.… [90m<tibble [48 × 9]>[39m     -[31m0[39m[31m.[39m[31m00[39m[31m6[4m4[24m[4m0[24m[39m     0.442   -[31m0[39m[31m.[39m[31m0[39m[31m14[4m5[24m[39m 0.988  
+## [90m 4[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      0.049[4m0[24m      0.555    0.088[4m4[24m 0.930  
+## [90m 5[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m     -[31m1[39m[31m.[39m[31m77[39m        0.553   -[31m3[39m[31m.[39m[31m21[39m   0.001[4m3[24m[4m4[24m
+## [90m 6[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      0.236       0.443    0.534  0.593  
+## [90m 7[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      2.63        1.38     1.91   0.056[4m1[24m 
+## [90m 8[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m     -[31m0[39m[31m.[39m[31m841[39m       0.526   -[31m1[39m[31m.[39m[31m60[39m   0.110  
+## [90m 9[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      0.959       0.608    1.58   0.114  
+## [90m10[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      1.52        0.614    2.47   0.013[4m4[24m 
 ## [90m# ℹ 12 more rows[39m

 
We can also perform test of Kaplan-Meier curves.

 
@@ -814,16 +814,16 @@ 
Test differential cell-type abund
 
## [90m# A tibble: 22 × 6[39m
 ##    .cell_type                       cell_type_proportions .low_cellularity_exp…¹
 ##    [3m[90m<chr>[39m[23m                            [3m[90m<list>[39m[23m                                 [3m[90m<dbl>[39m[23m
-## [90m 1[39m cibersort.B.cells.naive          [90m<tibble [48 × 9]>[39m                      12.2 
-## [90m 2[39m cibersort.B.cells.memory         [90m<tibble [48 × 9]>[39m                      13.7 
-## [90m 3[39m cibersort.Plasma.cells           [90m<tibble [48 × 9]>[39m                      12.0 
-## [90m 4[39m cibersort.T.cells.CD8            [90m<tibble [48 × 9]>[39m                      11.1 
-## [90m 5[39m cibersort.T.cells.CD4.naive      [90m<tibble [48 × 9]>[39m                       9.18
-## [90m 6[39m cibersort.T.cells.CD4.memory.re… [90m<tibble [48 × 9]>[39m                      10.7 
-## [90m 7[39m cibersort.T.cells.CD4.memory.ac… [90m<tibble [48 × 9]>[39m                      12.1 
-## [90m 8[39m cibersort.T.cells.follicular.he… [90m<tibble [48 × 9]>[39m                      18.3 
-## [90m 9[39m cibersort.T.cells.regulatory..T… [90m<tibble [48 × 9]>[39m                       9.90
-## [90m10[39m cibersort.T.cells.gamma.delta    [90m<tibble [48 × 9]>[39m                      17.7 
+## [90m 1[39m cibersort.B.cells.naive          [90m<tibble [48 × 9]>[39m                       11.0
+## [90m 2[39m cibersort.B.cells.memory         [90m<tibble [48 × 9]>[39m                       18.3
+## [90m 3[39m cibersort.Plasma.cells           [90m<tibble [48 × 9]>[39m                       12.3
+## [90m 4[39m cibersort.T.cells.CD8            [90m<tibble [48 × 9]>[39m                       13.4
+## [90m 5[39m cibersort.T.cells.CD4.naive      [90m<tibble [48 × 9]>[39m                       10.4
+## [90m 6[39m cibersort.T.cells.CD4.memory.re… [90m<tibble [48 × 9]>[39m                       12.5
+## [90m 7[39m cibersort.T.cells.CD4.memory.ac… [90m<tibble [48 × 9]>[39m                       14.7
+## [90m 8[39m cibersort.T.cells.follicular.he… [90m<tibble [48 × 9]>[39m                       19.0
+## [90m 9[39m cibersort.T.cells.regulatory..T… [90m<tibble [48 × 9]>[39m                       13.9
+## [90m10[39m cibersort.T.cells.gamma.delta    [90m<tibble [48 × 9]>[39m                       20.1
 ## [90m# ℹ 12 more rows[39m
 ## [90m# ℹ abbreviated name: ¹​.low_cellularity_expected[39m
 ## [90m# ℹ 3 more variables: .high_cellularity_expected <dbl>, pvalue <dbl>,[39m
diff --git a/pkgdown.yml b/pkgdown.yml
index 84e4125e..45fda8b1 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
   introduction: introduction.html
-last_built: 2024-05-16T05:09Z
+last_built: 2024-05-16T05:46Z
 
diff --git a/reference/figures/plot_cluster-1.png b/reference/figures/plot_cluster-1.png
index 149c6193..ea63166b 100644
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diff --git a/reference/figures/unnamed-chunk-14-1.png b/reference/figures/unnamed-chunk-14-1.png
index db88df68..0ccf997a 100644
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diff --git a/reference/figures/unnamed-chunk-19-1.png b/reference/figures/unnamed-chunk-19-1.png
index a7ef3416..7ebe3633 100644
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diff --git a/reference/test_differential_abundance-methods.html b/reference/test_differential_abundance-methods.html
index 6543c240..57e52eb8 100644
--- a/reference/test_differential_abundance-methods.html
+++ b/reference/test_differential_abundance-methods.html
@@ -422,7 +422,7 @@ 
Examples

   )
 #> 
 #> n = 5 samples, 2 individuals
-#> Time difference of 30.04662 secs
+#> Time difference of 31.05561 secs
 #> tidybulk says: to access the raw results (fitted GLM) do `attr(..., "internals")$glmmseq_lme4`
 #> class: SummarizedExperiment 
 #> dim: 40 5