diff --git a/404.html b/404.html index d36b44c..3f516c1 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ CytoMDS - 0.99.2 + 0.99.3 diff --git a/LICENSE-text.html b/LICENSE-text.html index 4115c44..ca27cb9 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ CytoMDS - 0.99.2 + 0.99.3 diff --git a/articles/CytoMDS.html b/articles/CytoMDS.html index 6f56a53..138e671 100644 --- a/articles/CytoMDS.html +++ b/articles/CytoMDS.html @@ -33,7 +33,7 @@ CytoMDS - 0.99.2 + 0.99.3 @@ -153,7 +153,7 @@

Session information## [7] purrr_1.0.2 textshaping_0.3.6 jsonlite_1.8.7 ## [10] glue_1.6.2 rprojroot_2.0.3 htmltools_0.5.6 ## [13] ragg_1.2.5 sass_0.4.7 rmarkdown_2.25 -## [16] evaluate_0.21 jquerylib_0.1.4 fastmap_1.1.1 +## [16] evaluate_0.22 jquerylib_0.1.4 fastmap_1.1.1 ## [19] lifecycle_1.0.3 yaml_2.3.7 memoise_2.0.1 ## [22] bookdown_0.35 BiocManager_1.30.22 stringr_1.5.0 ## [25] compiler_4.3.1 fs_1.6.3 systemfonts_1.0.4 diff --git a/articles/index.html b/articles/index.html index adf0110..1fe49cb 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ CytoMDS - 0.99.2 + 0.99.3 diff --git a/authors.html b/authors.html index 0851d9f..2997acf 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ CytoMDS - 0.99.2 + 0.99.3 @@ -74,13 +74,13 @@

Citation

Hauchamps P, Gatto L (2023). CytoMDS: Low Dimensions projection of cytometry samples. -R package version 0.99.2, https://uclouvain-cbio.github.io/CytoMDS. +R package version 0.99.3, https://uclouvain-cbio.github.io/CytoMDS. 

@Manual{,
   title = {CytoMDS: Low Dimensions projection of cytometry samples},
   author = {Philippe Hauchamps and Laurent Gatto},
   year = {2023},
-  note = {R package version 0.99.2},
+  note = {R package version 0.99.3},
   url = {https://uclouvain-cbio.github.io/CytoMDS},
 }
diff --git a/index.html b/index.html index efd0e0f..ffbd5f0 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ CytoMDS - 0.99.2 + 0.99.3 diff --git a/news/index.html b/news/index.html index ac9ed16..dc5738f 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ CytoMDS - 0.99.2 + 0.99.3 @@ -63,6 +63,11 @@

CytoMDS 0.99.2
  • use global Rsquare as an indicator of quality of projection
  • use %Var explained per axis
    • +
    +

    CytoMDS 0.99.3

    +
    diff --git a/pkgdown.yml b/pkgdown.yml index 76606dc..06869c2 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,7 +1,7 @@ pandoc: 3.1.1 pkgdown: 2.0.7.9000 -pkgdown_sha: c9206802f2888992de92aa41f517ba7812f05331 +pkgdown_sha: 170015984ae234da3028b2b083df757227fdd241 articles: CytoMDS: CytoMDS.html -last_built: 2023-09-28T14:38Z +last_built: 2023-10-04T09:23Z diff --git a/reference/CytoMDS.html b/reference/CytoMDS.html index df80d55..29f66bf 100644 --- a/reference/CytoMDS.html +++ b/reference/CytoMDS.html @@ -43,7 +43,7 @@ CytoMDS - 0.99.2 + 0.99.3 diff --git a/reference/computeMetricMDS.html b/reference/computeMetricMDS.html index 2030e0f..39fcc3e 100644 --- a/reference/computeMetricMDS.html +++ b/reference/computeMetricMDS.html @@ -5,9 +5,14 @@ (cmdscale alike, aka Torgerson's algorithm), but is the SMACOF algorithm for metric distances that are not necessarily euclidean. -Note that after the obtention of the projections on the nDim dimensions, +After having obtained the projections on the nDim dimensions, we always apply svd decomposition to visualize as first axes the ones that -contain the most variance of the projected dataset in nDim dimensions"> @@ -25,7 +30,7 @@ CytoMDS - 0.99.2 + 0.99.3 @@ -66,13 +71,25 @@

    metric MDS projection of sample

    (cmdscale alike, aka Torgerson's algorithm), but is the SMACOF algorithm for metric distances that are not necessarily euclidean. -Note that after the obtention of the projections on the nDim dimensions, +After having obtained the projections on the nDim dimensions, we always apply svd decomposition to visualize as first axes the ones that -contain the most variance of the projected dataset in nDim dimensions

    +contain the most variance of the projected dataset in nDim dimensions. +Instead of being provided directly by the user, the nDim parameter can +otherwise be found iteratively by finding the minimum nDim parameter that +allows the projection to reach a target pseudo RSquare. +If this is the case, the maxDim parameter is used to avoid +looking for too big projection spaces.

    - 
    computeMetricMDS(pwDist, nDim = 2, seed = NULL, ...)
    + 
    computeMetricMDS(
+  pwDist,
+  nDim = NULL,
+  seed = NULL,
+  targetPseudoRSq = 0.99,
+  maxDim = 128,
+  ...
+)
    @@ -84,7 +101,8 @@

    Arguments

    nDim
    -

    number of dimensions of projection, as input to SMACOF algorithm

    +

    number of dimensions of projection, as input to SMACOF algorithm +if not provided, will be found iteratively using targetPseudoRSq

    seed
    @@ -92,6 +110,16 @@

    Arguments

    (e.g. when init=="random" but not only)

    +
    targetPseudoRSq
    +

    target pseudo RSquare to be reached +(only used when nDim is set to NULL)

    + + +
    maxDim
    +

    in case nDim is found iteratively, +maximum number of dimensions the search procedure is allowed to explore

    + +
    ...

    additional parameters passed to SMACOF algorithm

    @@ -175,9 +203,13 @@

    Examples

    channels = c("FSC-A", "SSC-A"), verbose = FALSE) -# compute Metric MDS object +# compute Metric MDS object with explicit number of dimensions +mdsObj <- computeMetricMDS(pwDist, nDim = 2, seed = 0) -mdsObj <- computeMetricMDS(pwDist, seed = 0) +#' # compute Metric MDS object by reaching a target pseudo RSquare +mdsObj <- computeMetricMDS(pwDist, seed = 0, targetPseudoRSq = 0.999) +mdsObj$nDim # should be 3 +#> [1] 3
    diff --git a/reference/getChannelsSummaryStat.html b/reference/getChannelsSummaryStat.html index e34f4e7..2fe189b 100644 --- a/reference/getChannelsSummaryStat.html +++ b/reference/getChannelsSummaryStat.html @@ -18,7 +18,7 @@ CytoMDS - 0.99.2 + 0.99.3 diff --git a/reference/getEMDDist.html b/reference/getEMDDist.html index 24d18c0..8ec66dc 100644 --- a/reference/getEMDDist.html +++ b/reference/getEMDDist.html @@ -17,7 +17,7 @@ CytoMDS - 0.99.2 + 0.99.3 diff --git a/reference/getPairWiseEMDDist.html b/reference/getPairWiseEMDDist.html index 503b56f..866a64b 100644 --- a/reference/getPairWiseEMDDist.html +++ b/reference/getPairWiseEMDDist.html @@ -18,7 +18,7 @@ CytoMDS - 0.99.2 + 0.99.3 diff --git a/reference/index.html b/reference/index.html index 673f38f..a40448b 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ CytoMDS - 0.99.2 + 0.99.3