diff --git a/.Rbuildignore b/.Rbuildignore index d554f5c81..6c202dfd9 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,6 @@ *.tws *.md +^.*\.Rproj$ +^\.Rproj\.user$ +^LICENSE\.md$ +^_notes$ diff --git a/.gitignore b/.gitignore index 86226d321..014f83228 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,3 @@ *.tws +.Rproj.user +_notes diff --git a/DESCRIPTION b/DESCRIPTION index 1a7f8889e..f08b292ef 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,15 +1,15 @@ Package: curatedPCaData -Title: curated Prostate Cancer Data +Title: Curated Prostate Cancer Data Version: 0.0-2 Date: 2020-04-03 -Authors@R: person("First", "Last", email = "first.last@example.com", +Authors@R: person("Daniel", "Laajala", email = "teelaa@utu.fi.com", role = c("aut", "cre")) Maintainer: -Description: Foo Bar +Description: A selection of annotated prostate cancer datasets. Depends: R (>= 3.1.0), S4Vectors (>= 0.23.18) Imports: cgdsr, annotate, org.Hs.eg.db, biomaRt, GenomicFeatures, GEOquery Suggests: -License: GPL (>= 3) +License: GPL-3 Encoding: UTF-8 RoxygenNote: 6.1.1 VignetteBuilder: R.rsp diff --git a/README.Rmd b/README.Rmd new file mode 100644 index 000000000..ddc002e59 --- /dev/null +++ b/README.Rmd @@ -0,0 +1,42 @@ +--- +output: github_document +--- + +```{r setup, include = FALSE} + +knitr::opts_chunk$set( + collapse = TRUE, + fig.path = "man/figures/README-", + out.width = "100%" +) + +``` + +# curatedPCaData + + + + +## Overview + +`curatedPCaData` is a collection of publically available and annotated data resources +concerning prostate cancer. + +## Installation + +You can install `curatedPCaData` from github with: + +```r +# install.packages("devtools") +devtools::install_github("Syksy/curatedPCaData") +``` + + + +## Usage + +```{r, eval=FALSE} +library(curatedPCaData) + +# insert basic example here +``` \ No newline at end of file diff --git a/README.md b/README.md index a901b11d0..690df5d6c 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,30 @@ -# curatedPCaData -Curated Prostate Cancer Data R-package / pipelines / workspaces + +# curatedPCaData + + + + + +## Overview + +`curatedPCaData` is a collection of publically available and annotated +data resources concerning prostate cancer. + +## Installation + +You can install `curatedPCaData` from github with: + +``` r +# install.packages("devtools") +devtools::install_github("Syksy/curatedPCaData") +``` + + + +## Usage + +``` r +library(curatedPCaData) + +# insert basic example here +``` diff --git a/curatedPCaData.Rproj b/curatedPCaData.Rproj new file mode 100644 index 000000000..21a4da087 --- /dev/null +++ b/curatedPCaData.Rproj @@ -0,0 +1,17 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source diff --git a/man/figures/hex.png b/man/figures/hex.png new file mode 100644 index 000000000..7e547d644 Binary files /dev/null and b/man/figures/hex.png differ diff --git a/man/figures/hex_sticker.R b/man/figures/hex_sticker.R new file mode 100644 index 000000000..1bd7d56d9 --- /dev/null +++ b/man/figures/hex_sticker.R @@ -0,0 +1,12 @@ +library(hexSticker) +library(magick) + +# image from : https://icon-icons.com/icon/tumor-cancer-human-biology-disease-medical-health-cell/133488 +imgurl <- "man/figures/tumor.png" + +sticker(imgurl, + package="curatedPCaData", p_size=5, p_color = "#FB62AC", p_y = 0.6, + s_x=1, s_y=1.2, s_width=.6, + h_fill = "white", h_color = "#2B2671", + url = "https://github.com/Syksy/curatedPCaData", u_color = "#FB62AC", u_size = 1, + filename="man/figures/hex.png") \ No newline at end of file diff --git a/man/figures/tumor.png b/man/figures/tumor.png new file mode 100644 index 000000000..d11db815c Binary files /dev/null and b/man/figures/tumor.png differ