diff --git a/articles/figures/fig_1.png b/articles/figures/fig_1.png new file mode 100644 index 0000000..64aaba6 Binary files /dev/null and b/articles/figures/fig_1.png differ diff --git a/articles/technical_details.html b/articles/technical_details.html index 95bbb2b..a21a6d4 100644 --- a/articles/technical_details.html +++ b/articles/technical_details.html @@ -77,17 +77,17 @@

Technical details

-
-Figure 1: Left: One simulated dataset generated according to -\(\mathcal{MN}_{100\times -2}(\textbf{0}_{100\times 2}, \textbf{I}_{100}, \sigma^2 -\textbf{I}_{2})\). We apply \(k\)-means clustering to obtain three -clusters. The cluster centroids are displayed as triangles. -Center: Quantile-quantile plot of the Wald p-values applied to -2,000 simulated datasets from \(\mathcal{MN}_{100\times 2}(\textbf{0}_{100\times -2}, \textbf{I}_{100}, \sigma^2 \textbf{I}_{2})\). Right: -Quantile-quantile plot of our proposed p-values applied to the same -simulated datasets as in center. +
+Figure 1: We simulated one dataset according to \(\mathcal{MN}_{100\times 10}(\textbf{\mu}, +\textbf{I}_{100}, \Sigma)\), where \(\mu_i = (1,0_9)^T\) for \(i=1,\ldots, 50\) and \(\mu_i = (0_9,1)^T\) for \(i=51,\ldots, 100\), and \(\Sigma_{ij} = 1\{i=j\}+0.4\cdot 1\{i\neq +j\}\). (a): Empirical distribution of feature 2 based on +the simulated data set. In this case, all observations have the same +mean for feature 2. (b): We apply k-means clustering to obtain +two clusters and plot the empirical distribution of feature 2 stratified +by the clusters. (c): Quantile-quantile plot of naive z-test +(black) our proposed p-values (orange) applied to the simulated data +sets for testing the null hypotheses for a difference in means for +features 2–8.
diff --git a/index.html b/index.html index 1abde2b..786b748 100644 --- a/index.html +++ b/index.html @@ -66,7 +66,7 @@
-

CADET (Clustering And Differential Expression Testing) +

CADET (Clustering And Differential Expression Testing)

What is CADET? diff --git a/pkgdown.yml b/pkgdown.yml index 0a783d1..30a1284 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -4,7 +4,7 @@ pkgdown_sha: ~ articles: Tutorials: Tutorials.html technical_details: technical_details.html -last_built: 2023-11-25T23:21Z +last_built: 2023-11-25T23:51Z urls: reference: https://yiqunchen.github.io/CADET/reference article: https://yiqunchen.github.io/CADET/articles diff --git a/reference/figures/cadet_sticker.png b/reference/figures/cadet_sticker.png new file mode 100644 index 0000000..4e7cf4f Binary files /dev/null and b/reference/figures/cadet_sticker.png differ diff --git a/reference/test_hier_clusters_exact_1f.html b/reference/test_hier_clusters_exact_1f.html index ae34fc4..7ba473d 100644 --- a/reference/test_hier_clusters_exact_1f.html +++ b/reference/test_hier_clusters_exact_1f.html @@ -169,17 +169,31 @@

Examples

# with respect to the 1st feature test_hier_clusters_exact_1f(X=dat, link="average", hcl=hcl, K=3, k1=1, k2=2, feat=1) #> $stat -#> [1] 0.9469145 +#> [1] -0.9469145 +#> +#> $cluster_1 +#> [1] 1 +#> +#> $cluster_2 +#> [1] 2 #> #> $pval #> [1] 1.001053e-06 #> +#> $p_naive +#> [1] 2.002035e-06 +#> #> $trunc #> Object of class Intervals #> 2 intervals over R: #> (-Inf, 0.791767114050557) #> (4.48600166611002, Inf) #> +#> $linkage +#> [1] "average" +#> +#> attr(,"class") +#> [1] "hier_inference"