From c5e2905eaaa3067db8a594f55f98d1be4dbce6dd Mon Sep 17 00:00:00 2001 From: Myles Lewis Date: Tue, 5 Jul 2022 15:24:56 +0100 Subject: [PATCH] Update links --- R/add_animation.R | 2 +- R/boxplot_trio.R | 2 +- R/example_data.R | 4 ++-- R/polar_grid.R | 2 +- R/radial_ggplot.R | 2 +- R/radial_plotly.R | 2 +- R/show_grid.R | 2 +- R/significance_subset.R | 2 +- R/volcano3D.R | 2 +- man/add_animation.Rd | 2 +- man/boxplot_trio.Rd | 2 +- man/polar_grid.Rd | 2 +- man/radial_ggplot.Rd | 2 +- man/radial_plotly.Rd | 2 +- man/show_grid.Rd | 2 +- man/significance_subset.Rd | 2 +- man/syn_example_meta.Rd | 2 +- man/syn_example_rld.Rd | 2 +- man/volcano3D.Rd | 2 +- 19 files changed, 20 insertions(+), 20 deletions(-) diff --git a/R/add_animation.R b/R/add_animation.R index 4950c507..a7a09d6a 100644 --- a/R/add_animation.R +++ b/R/add_animation.R @@ -19,7 +19,7 @@ #' z-axis #' @references #' Lewis, Myles J., et al. (2019). -#' \href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +#' \href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ #' Molecular portraits of early rheumatoid arthritis identify clinical and #' treatment response phenotypes.} #' \emph{Cell reports}, \strong{28}:9 diff --git a/R/boxplot_trio.R b/R/boxplot_trio.R index e2353428..cb8735c2 100644 --- a/R/boxplot_trio.R +++ b/R/boxplot_trio.R @@ -48,7 +48,7 @@ #' @keywords hplot #' @references #' Lewis, Myles J., et al. (2019). -#' \href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +#' \href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ #' Molecular portraits of early rheumatoid arthritis identify clinical and #' treatment response phenotypes.} #' \emph{Cell reports}, \strong{28}:9 diff --git a/R/example_data.R b/R/example_data.R index 46bf1ee0..edba6e38 100644 --- a/R/example_data.R +++ b/R/example_data.R @@ -7,7 +7,7 @@ #' \describe{ #' \item{Pathotype}{The synovial biopsy histological pathotype} #' } -#' @source \url{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1 +#' @source \url{https://pubmed.ncbi.nlm.nih.gov/31461658/ #' } "syn_example_meta" @@ -18,7 +18,7 @@ #' #' @format A data frame with 500 rows representing the most significant #' genes/probes and 81 columns representing samples. -#' @source \url{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1 +#' @source \url{https://pubmed.ncbi.nlm.nih.gov/31461658/ #' } "syn_example_rld" diff --git a/R/polar_grid.R b/R/polar_grid.R index b8ad26fa..2cfa0e8a 100644 --- a/R/polar_grid.R +++ b/R/polar_grid.R @@ -61,7 +61,7 @@ setClass("grid", slots = list( #' } #' @references #' Lewis, Myles J., et al. (2019). -#' \href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +#' \href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ #' Molecular portraits of early rheumatoid arthritis identify clinical and #' treatment response phenotypes.} #' \emph{Cell reports}, \strong{28}:9 diff --git a/R/radial_ggplot.R b/R/radial_ggplot.R index 8e90a0c0..000aff86 100644 --- a/R/radial_ggplot.R +++ b/R/radial_ggplot.R @@ -40,7 +40,7 @@ #' @keywords hplot #' @references #' Lewis, Myles J., et al. (2019). -#' \href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +#' \href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ #' Molecular portraits of early rheumatoid arthritis identify clinical and #' treatment response phenotypes.} #' \emph{Cell reports}, \strong{28}:9 diff --git a/R/radial_plotly.R b/R/radial_plotly.R index b11f3de3..a95a07e6 100644 --- a/R/radial_plotly.R +++ b/R/radial_plotly.R @@ -39,7 +39,7 @@ #' @importFrom methods is #' @references #' Lewis, Myles J., et al. (2019). -#' \href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +#' \href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ #' Molecular portraits of early rheumatoid arthritis identify clinical and #' treatment response phenotypes.} #' \emph{Cell reports}, \strong{28}:9 diff --git a/R/show_grid.R b/R/show_grid.R index b4a3e413..42cf55d3 100644 --- a/R/show_grid.R +++ b/R/show_grid.R @@ -10,7 +10,7 @@ #' @importFrom plotly plot_ly add_trace add_text layout %>% #' @references #' Lewis, Myles J., et al. (2019). -#' \href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +#' \href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ #' Molecular portraits of early rheumatoid arthritis identify clinical and #' treatment response phenotypes.} #' \emph{Cell reports}, \strong{28}:9 diff --git a/R/significance_subset.R b/R/significance_subset.R index d70edd58..6fc1fa0f 100644 --- a/R/significance_subset.R +++ b/R/significance_subset.R @@ -10,7 +10,7 @@ #' object. #' @references #' Lewis, Myles J., et al. (2019). -#' \href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +#' \href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ #' Molecular portraits of early rheumatoid arthritis identify clinical and #' treatment response phenotypes.} #' \emph{Cell reports}, \strong{28}:9 diff --git a/R/volcano3D.R b/R/volcano3D.R index 82d5db5c..b4c7a990 100644 --- a/R/volcano3D.R +++ b/R/volcano3D.R @@ -49,7 +49,7 @@ #' z-axis #' @references #' Lewis, Myles J., et al. (2019). -#' \href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +#' \href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ #' Molecular portraits of early rheumatoid arthritis identify clinical and #' treatment response phenotypes.} #' \emph{Cell reports}, \strong{28}:9 diff --git a/man/add_animation.Rd b/man/add_animation.Rd index 522b0f43..c0af6c0f 100644 --- a/man/add_animation.Rd +++ b/man/add_animation.Rd @@ -56,7 +56,7 @@ add_animation(p) } \references{ Lewis, Myles J., et al. (2019). -\href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +\href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes.} \emph{Cell reports}, \strong{28}:9 diff --git a/man/boxplot_trio.Rd b/man/boxplot_trio.Rd index 62e679c0..cf26319f 100644 --- a/man/boxplot_trio.Rd +++ b/man/boxplot_trio.Rd @@ -82,7 +82,7 @@ boxplot_trio(syn_polar, value = "COBL") } \references{ Lewis, Myles J., et al. (2019). -\href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +\href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes.} \emph{Cell reports}, \strong{28}:9 diff --git a/man/polar_grid.Rd b/man/polar_grid.Rd index 870f5fcd..57e361cf 100644 --- a/man/polar_grid.Rd +++ b/man/polar_grid.Rd @@ -71,7 +71,7 @@ grid <- polar_grid(r_vector=syn_polar@df[[1]]$r, } \references{ Lewis, Myles J., et al. (2019). -\href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +\href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes.} \emph{Cell reports}, \strong{28}:9 diff --git a/man/radial_ggplot.Rd b/man/radial_ggplot.Rd index b9fe8c99..3383ff09 100644 --- a/man/radial_ggplot.Rd +++ b/man/radial_ggplot.Rd @@ -94,7 +94,7 @@ radial_ggplot(polar = syn_polar, label_rows = c("COBL")) } \references{ Lewis, Myles J., et al. (2019). -\href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +\href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes.} \emph{Cell reports}, \strong{28}:9 diff --git a/man/radial_plotly.Rd b/man/radial_plotly.Rd index 16ce0d03..009d7910 100644 --- a/man/radial_plotly.Rd +++ b/man/radial_plotly.Rd @@ -95,7 +95,7 @@ radial_plotly(polar = syn_polar, label_rows = c("COBL")) } \references{ Lewis, Myles J., et al. (2019). -\href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +\href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes.} \emph{Cell reports}, \strong{28}:9 diff --git a/man/show_grid.Rd b/man/show_grid.Rd index 6f1af15c..75d7cfc6 100644 --- a/man/show_grid.Rd +++ b/man/show_grid.Rd @@ -37,7 +37,7 @@ p$cyl } \references{ Lewis, Myles J., et al. (2019). -\href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +\href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes.} \emph{Cell reports}, \strong{28}:9 diff --git a/man/significance_subset.Rd b/man/significance_subset.Rd index 53a673d8..014732d5 100644 --- a/man/significance_subset.Rd +++ b/man/significance_subset.Rd @@ -29,7 +29,7 @@ subset <- significance_subset(syn_polar, "L+", "df") } \references{ Lewis, Myles J., et al. (2019). -\href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +\href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes.} \emph{Cell reports}, \strong{28}:9 diff --git a/man/syn_example_meta.Rd b/man/syn_example_meta.Rd index 074e31e9..08b4e846 100644 --- a/man/syn_example_meta.Rd +++ b/man/syn_example_meta.Rd @@ -11,7 +11,7 @@ A data frame with 81 rows and 1 variables: } } \source{ -\url{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1 +\url{https://pubmed.ncbi.nlm.nih.gov/31461658/ } } \usage{ diff --git a/man/syn_example_rld.Rd b/man/syn_example_rld.Rd index b765880c..9e7b7069 100644 --- a/man/syn_example_rld.Rd +++ b/man/syn_example_rld.Rd @@ -9,7 +9,7 @@ A data frame with 500 rows representing the most significant genes/probes and 81 columns representing samples. } \source{ -\url{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1 +\url{https://pubmed.ncbi.nlm.nih.gov/31461658/ } } \usage{ diff --git a/man/volcano3D.Rd b/man/volcano3D.Rd index 5eaeca1f..1d387314 100644 --- a/man/volcano3D.Rd +++ b/man/volcano3D.Rd @@ -113,7 +113,7 @@ volcano3D(syn_polar) } \references{ Lewis, Myles J., et al. (2019). -\href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{ +\href{https://pubmed.ncbi.nlm.nih.gov/31461658/}{ Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes.} \emph{Cell reports}, \strong{28}:9