diff --git a/README.md b/README.md index 8bfea42..e9cd8c2 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ [![R build status](https://github.com/pneuvial/adjclust/workflows/R-CMD-check/badge.svg)](https://github.com/pneuvial/adjclust/actions) [![Coverage -Status](https://codecov.io/gh/pneuvial/adjclust/branch/develop/graph/badge.svg)](https://app.codecov.io/gh/pneuvial/adjclust/tree/develop) +Status](https://img.shields.io/codecov/c/github/pneuvial/adjclust/develop.svg)](https://codecov.io/github/pneuvial/adjclust/branch/develop) `adjclust` is a package that provides methods to perform adjacency-constrained hierarchical agglomerative clustering. @@ -76,10 +76,9 @@ image(ld.ceph, lwd = 0) fit <- snpClust(geno, stats = "R.squared", h = h) #> Warning in run.snpClust(x, h = h, stats = stats): Forcing the LD similarity to #> be smaller than or equal to 1 -#> as(, "dgTMatrix") is deprecated since Matrix 1.4-2; do as(., "generalMatrix") instead #> Note: 133 merges with non increasing heights. plot(fit) -#> Warning in plot.chac(fit): +#> Warning: #> Detected reversals in dendrogram: mode = 'corrected', 'within-disp' or 'total-disp' might be more relevant. ``` @@ -88,6 +87,9 @@ plot(fit) ``` r sel_clust <- select(fit, "bs") plotSim(as.matrix(ld.ceph), clustering = sel_clust, dendro = fit) +#> Warning: +#> Detected reversals in dendrogram: mode = 'corrected', 'within-disp' or 'total-disp' might be more relevant. +#> Warning: Removed 602 rows containing missing values (`geom_text()`). ``` ![](man/figures/README-snpClust-3.png) @@ -118,7 +120,7 @@ mapC(binned) fitB <- hicClust(binned) #> Note: 5 merges with non increasing heights. plot(fitB) -#> Warning in plot.chac(fitB): +#> Warning: #> Detected reversals in dendrogram: mode = 'corrected', 'within-disp' or 'total-disp' might be more relevant. ``` @@ -126,6 +128,9 @@ plot(fitB) ``` r plotSim(intdata(binned), dendro = fitB) # default: log scale for colors +#> Warning: +#> Detected reversals in dendrogram: mode = 'corrected', 'within-disp' or 'total-disp' might be more relevant. +#> Warning: Removed 41 rows containing missing values (`geom_text()`). ``` ![](man/figures/README-hicClust-3.png) diff --git a/man/figures/README-adjClust-1.png b/man/figures/README-adjClust-1.png index ff7bd37..c23e596 100644 Binary files a/man/figures/README-adjClust-1.png and b/man/figures/README-adjClust-1.png differ diff --git a/man/figures/README-hicClust-1.png b/man/figures/README-hicClust-1.png index 44007c4..f8b679e 100644 Binary files a/man/figures/README-hicClust-1.png and b/man/figures/README-hicClust-1.png differ diff --git a/man/figures/README-hicClust-2.png b/man/figures/README-hicClust-2.png index 0cbeae1..2212f33 100644 Binary files a/man/figures/README-hicClust-2.png and b/man/figures/README-hicClust-2.png differ diff --git a/man/figures/README-hicClust-3.png b/man/figures/README-hicClust-3.png index a77f33f..57c0ebf 100644 Binary files a/man/figures/README-hicClust-3.png and b/man/figures/README-hicClust-3.png differ diff --git a/man/figures/README-snpClust-1.png b/man/figures/README-snpClust-1.png index 1a0ef12..3a8bd81 100644 Binary files a/man/figures/README-snpClust-1.png and b/man/figures/README-snpClust-1.png differ diff --git a/man/figures/README-snpClust-2.png b/man/figures/README-snpClust-2.png index 054908e..4a94c68 100644 Binary files a/man/figures/README-snpClust-2.png and b/man/figures/README-snpClust-2.png differ diff --git a/man/figures/README-snpClust-3.png b/man/figures/README-snpClust-3.png index f1a3842..a934b4c 100644 Binary files a/man/figures/README-snpClust-3.png and b/man/figures/README-snpClust-3.png differ