From 2c7c1c7e67ab93369c94b1e07ef51199e7e825ed Mon Sep 17 00:00:00 2001 From: Bharath Air Date: Tue, 28 May 2024 15:14:23 +0200 Subject: [PATCH] Fixed problem with latex in README and customized the site. --- README.Rmd | 2 +- README.md | 6 ++--- _pkgdown.yml | 13 +++++++++- docs/404.html | 7 ++---- docs/LICENSE.html | 7 ++---- docs/articles/UserGuide.html | 7 ++---- docs/articles/index.html | 7 ++---- docs/authors.html | 7 ++---- docs/extra.css | 12 +++++++-- docs/index.html | 9 +++---- docs/pkgdown.yml | 2 +- docs/reference/compareRhythms.html | 7 ++---- docs/reference/compareRhythms_cosinor.html | 7 ++---- docs/reference/compareRhythms_deseq2.html | 7 ++---- docs/reference/compareRhythms_dodr.html | 7 ++---- docs/reference/compareRhythms_edgeR.html | 7 ++---- docs/reference/compareRhythms_limma.html | 7 ++---- .../compareRhythms_model_select.html | 7 ++---- docs/reference/compareRhythms_voom.html | 7 ++---- docs/reference/high_fat_diet_ma.html | 7 ++---- docs/reference/high_fat_diet_rnaseq.html | 7 ++---- docs/reference/index.html | 25 +++++++++++++------ docs/search.json | 2 +- 23 files changed, 78 insertions(+), 98 deletions(-) diff --git a/README.Rmd b/README.Rmd index 1760953..bbb5b6f 100644 --- a/README.Rmd +++ b/README.Rmd @@ -34,7 +34,7 @@ cat( -The goal of *compareRhythms* is to find features with altered circadian rhythm parameters (*amplitude* and *phase*) between the control and experimental groups. A fit of the function $A\cos(\frac{2\pi t}{24} - \phi)$ to the data defines the rhythm parameters amplitude ($A$) and phase ($\phi$). +The goal of *compareRhythms* is to find features with altered circadian rhythm parameters (*amplitude* and *phase*) between the control and experimental groups. A fit of the function $A\cos(2\pi t/24 - \phi)$ to the data defines the rhythm parameters amplitude ($A$) and phase ($\phi$). ## Installation diff --git a/README.md b/README.md index 46efd83..5df9f09 100644 --- a/README.md +++ b/README.md @@ -16,9 +16,9 @@ GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-pro The goal of *compareRhythms* is to find features with altered circadian rhythm parameters (*amplitude* and *phase*) between the control and -experimental groups. A fit of the function -$A\cos(\frac{2\pi t}{24} - \phi)$ to the data defines the rhythm -parameters amplitude ($A$) and phase ($\phi$). +experimental groups. A fit of the function $A\cos(2\pi t/24 - \phi)$ to +the data defines the rhythm parameters amplitude ($A$) and phase +($\phi$). ## Installation diff --git a/_pkgdown.yml b/_pkgdown.yml index 7bf2dfc..34e8f15 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -4,4 +4,15 @@ template: bootswatch: flatly bslib: pkgdown-nav-height: 75px - +navbar: + components: + articles: + text: User guide + href: articles/UserGuide.html +reference: + - title: "Main function" + contents: + - compareRhythms + - title: "Datasets" + contents: + - starts_with("high_fat") diff --git a/docs/404.html b/docs/404.html index 0015b57..8d0a208 100644 --- a/docs/404.html +++ b/docs/404.html @@ -44,11 +44,8 @@
  • Reference
    • -
  • - -
    - Analyzing rhythmic data with compareRhythms -
    +
  • + User guide
    • diff --git a/docs/articles/UserGuide.html b/docs/articles/UserGuide.html index a91243e..7b0776a 100644 --- a/docs/articles/UserGuide.html +++ b/docs/articles/UserGuide.html @@ -46,11 +46,8 @@
  • Reference
    • -
  • - -
    - Analyzing rhythmic data with compareRhythms -
    +
  • + User guide
    • diff --git a/docs/authors.html b/docs/authors.html index 83668f1..1f46ead 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -21,11 +21,8 @@ diff --git a/docs/extra.css b/docs/extra.css index 0659eec..a1b4c43 100644 --- a/docs/extra.css +++ b/docs/extra.css @@ -1,7 +1,15 @@ h1 { - font-size: 36px; + font-size: 32px; } h2 { - font-size: 28px; + font-size: 24px; +} + +h3 { + font-size: 20px; +} + +h4 { + font-size: 16px; } diff --git a/docs/index.html b/docs/index.html index 9e716a8..34bb726 100644 --- a/docs/index.html +++ b/docs/index.html @@ -46,11 +46,8 @@
  • Reference
    • -
  • - -
    - Analyzing rhythmic data with compareRhythms -
    +
  • + User guide
    • -

    All functions

    +

    Main function

    @@ -62,7 +59,18 @@

    All functionscompareRhythms()
    Run differential rhythmicity analysis
    -
    +

    +

    Datasets

    + + + + +
    + + + + +
    high_fat_diet_ma
    @@ -73,7 +81,8 @@

    All functions