version 0.1.0

DESCRIPTION

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+Package: corrViz
+Type: Package
+Title: Visualise Correlations
+Version: 0.1.0
+Author: Alan Inglis
+Maintainer: Alan Inglis <alan.n.inglis@gmail.com>
+Description: An investigative tool designed to help users visualize correlations between variables in their datasets. This package aims to provide an easy and effective way to explore and visualize these correlations, making it easier to interpret and communicate results.
+License: GPL (>= 2)
+Encoding: UTF-8
+Imports: ggplot2, stats, grDevices, visNetwork, plotly, DendSer,
+        gganimate, igraph, ggraph, circlize, GGally, purrr, shiny
+RoxygenNote: 7.2.3
+Suggests: knitr, rmarkdown, scales, gifski
+VignetteBuilder: knitr
+NeedsCompilation: no
+Packaged: 2023-06-29 15:47:40 UTC; alaninglis
+Repository: CRAN
+Date/Publication: 2023-06-30 11:40:07 UTC

MD5

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+bab24dff6d81ef7cbee61b2b31942774 *DESCRIPTION
+bae140e33dfdba1b82cfaf674332705d *NAMESPACE
+795cc78bde4a39fddc941d5206752171 *R/animSolar.R
+d30ac5104d19994e8c9ec5dbe0358489 *R/corrBarplot.R
+79e163633f55b21e6ebe8aacf1ccaefd *R/corrBubble.R
+a9e74694dd5220dada05da64ce074ad3 *R/corrChord.R
+107c554f014794777bddd83c69eed964 *R/corrCircle.R
+038cf8b4d8f0f9246fec4788d3b08474 *R/corrGrid.R
+5b42f2e6c09b1376776ce31d3d3491a2 *R/corrHeatmap.R
+c4bafdd485c3f372551b60ece8d4399d *R/corrNetwork.R
+6ebd2a67134b28fc6632ce24e6daf4ef *R/corrPairs.R
+b78ece3f0194d8204bf223912c9cbb09 *R/corrSankey.R
+0523eac9ddea0f6b2f9aca01700018c2 *R/corrShiny.R
+9fb3f592f67879a268e6032c7aa413a3 *R/corrSolar.R
+206a4b0c222a57f203b5b7d73e2df90d *R/matrix2long.R
+64b753eba49192f9f525363ddb151271 *README.md
+8aa0349e09e9cd9daf03f2431e883d57 *build/vignette.rds
+29ca88effccbfe979bf4f3adf99eb2e3 *inst/doc/corrViz.R
+e729fdb7773ef2c756e9d7508d5593c5 *inst/doc/corrViz.Rmd
+6b4eec60a1ec0d54450bfeda5e471ae3 *inst/doc/corrViz.html
+5afbee77bdce7f5870043d005552b1ba *man/animSolar.Rd
+9912dee19f1dac10f87a24ff2594646d *man/corrBarplot.Rd
+71960c9427e2f91f72a8b2ea19857aa5 *man/corrBubble.Rd
+5d4bbcdc50a1c35f1f284269676c0b19 *man/corrChord.Rd
+518d885739dfb6a3ba217f3345adb325 *man/corrCircle.Rd
+8deb9c36711592750c2eb3156645ffbf *man/corrGrid.Rd
+9849aaefc8b35f1a4e8a2ccf13cb945e *man/corrHeatmap.Rd
+a677058b52c1c2de4fc2da1795c43e9e *man/corrNetwork.Rd
+10c49ec87185c687dbdb3b655f4c25de *man/corrPairs.Rd
+b249af21fe155bffe721c8061641308a *man/corrSankey.Rd
+ad8def40b092d8223d222550ec5f7159 *man/corrShiny.Rd
+e062ea9e401a7c9510b6015401e02da1 *man/corrSolar.Rd
+52f9cce159f1facba482d84cfe921122 *man/figures/README-chord-1.png
+491dac80c3a9d6a169ae720d76b2b8c0 *man/figures/README-chord2-1.png
+276183789e0c829040c3e117cda5dcdc *man/figures/README-circle-1.png
+f5ca8df2fe792d5c94f382947ad40e88 *man/figures/README-circle2-1.png
+1b37298d86c70ebd8909596cb615eaf2 *man/figures/README-solar-1.png
+775b1a8574f6d4420a05f7f18c948502 *man/matrix2long.Rd
+e729fdb7773ef2c756e9d7508d5593c5 *vignettes/corrViz.Rmd

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(animSolar)
+export(corrBarplot)
+export(corrBubble)
+export(corrChord)
+export(corrCircle)
+export(corrGrid)
+export(corrHeatmap)
+export(corrNetwork)
+export(corrPairs)
+export(corrSankey)
+export(corrShiny)
+export(corrSolar)
+export(matrix2long)
+import(ggplot2)
+import(ggraph)
+import(shiny)
+importFrom(DendSer,dser)
+importFrom(GGally,eval_data_col)
+importFrom(GGally,ggpairs)
+importFrom(GGally,wrap)
+importFrom(circlize,chordDiagram)
+importFrom(circlize,colorRamp2)
+importFrom(gganimate,anim_save)
+importFrom(gganimate,animate)
+importFrom(gganimate,gifski_renderer)
+importFrom(gganimate,transition_manual)
+importFrom(ggplot2,aes_string)
+importFrom(ggplot2,annotate)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_smooth)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_color_continuous)
+importFrom(ggplot2,scale_color_discrete)
+importFrom(ggplot2,scale_size_continuous)
+importFrom(ggplot2,scale_size_discrete)
+importFrom(grDevices,colorRampPalette)
+importFrom(grDevices,rainbow)
+importFrom(igraph,graph_from_data_frame)
+importFrom(plotly,ggplotly)
+importFrom(plotly,plot_ly)
+importFrom(plotly,style)
+importFrom(purrr,pmap)
+importFrom(stats,as.dist)
+importFrom(stats,cor)
+importFrom(stats,cor.test)
+importFrom(stats,na.omit)
+importFrom(stats,reshape)
+importFrom(visNetwork,visEdges)
+importFrom(visNetwork,visIgraphLayout)
+importFrom(visNetwork,visInteraction)
+importFrom(visNetwork,visLegend)
+importFrom(visNetwork,visNetwork)
+importFrom(visNetwork,visNodes)
+importFrom(visNetwork,visOptions)
+importFrom(visNetwork,visPhysics)

R/animSolar.R

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+#' animSolar
+#'
+#' This function creates an animated solar system plot of correlations between
+#' variables in a dataset.
+#'
+#' @param mat A square correlation matrix to visualise.
+#' @param sun A character string specifying the column name in the dataset to be treated
+#' as the 'sun' in the solar system plot.
+#' @param export A logical value specifying whether to export the animation as a GIF file, default is FALSE.
+#' @param num_frames An integer specifying the number of frames in the animation, default is 100.
+#' @param path A character string specifying the directory path where the GIF file will be saved, default is NULL.
+#' @param gif_name A character string specifying the name of the GIF file. Must be in the format "myFile.gif"
+#' @param fps An integer specifying the frames per second for the animation.
+#' Default is 60 and is only used when exporting a gif via \code{export = TRUE}.
+#'
+#'
+#' @details In a solar system correlation plot, the dependent variable of
+#' interest is positioned at the center, represented as the sun.
+#' The explanatory variables are depicted as planets orbiting
+#' around the sun, with their distance from the sun corresponding
+#' to the absolute value of their correlation with the dependent variable.
+#' Therefore, the greater the distance of a planet from the sun,
+#' the weaker the correlation between the explanatory variable
+#' and the dependent variable.
+#'
+#' @details The \code{num_frames} argument is used to select the number of frames.
+#' Setting this to a low value will produce the plot
+#' quicker, however having a low number of frames will result in the "planets" jumping
+#' as the frames transition. Additionally, a low values of   \code{num_frames} will affect the
+#' orbit of the animation when setting \code{export = FALSE}. This differs from the
+#' \code{fps} argument which sets the number of frames to play per second for use
+#' when exporting a gif.
+#'
+#' @return An animated solar system plot displaying correlations.
+#'
+#'
+#' @importFrom gganimate transition_manual
+#' @importFrom gganimate animate
+#' @importFrom gganimate anim_save
+#' @importFrom gganimate gifski_renderer
+#' @importFrom stats cor
+#' @importFrom stats na.omit
+#' @import ggplot2
+#'
+#' @examples
+#' cm <- cor(mtcars)
+#'
+#' animSolar(mat = cm,
+#'           sun = 'mpg',
+#'           export = FALSE,
+#'           num_frames = 25)
+#'
+#' @export
+animSolar <- function(mat,
+                      sun = NULL,
+                      export = FALSE,
+                      num_frames = 100,
+                      path = NULL,
+                      gif_name = "solar_system.gif",
+                      fps = 60) {
+  if(export){
+    if (!requireNamespace("gifski", quietly = TRUE)) {
+      stop('ERROR: gifski package is required to render animation.
+        Please use: install.packages("gifski")')
+    }
+  }
+
+  # declare global vars
+  colr <- col_name <- NULL
+
+  # Calculate correlation matrix
+  cor_matrix <- mat #cor(data, method = method)
+  diag(cor_matrix) <- NA
+
+  # Convert matrix to data frame
+  df_data_long <- matrix2long(cor_matrix)
+
+  # Filter rows where col_name equals 'sun'
+  df_data_filtered <- subset(df_data_long, col_name == sun)
+
+  # Order rows by 'value' column in descending order
+  df_data_ordered <- df_data_filtered[order(df_data_filtered$value, decreasing = TRUE),]
+
+  # Rename columns
+  names(df_data_ordered)[names(df_data_ordered) == "value"] <- "r"
+  names(df_data_ordered)[names(df_data_ordered) == "col_name"] <- "x"
+  names(df_data_ordered)[names(df_data_ordered) == "row_name"] <- "y"
+
+  # Assign the result to correlations
+  correlations <- df_data_ordered
+
+  # check if any correaltions would round to 1 and change to 0.9
+  correlations$r <- ifelse(correlations$r > 0.9, 0.9, correlations$r)
+
+
+  # Assign orbit radius based on absolute, rounded correlation values
+  correlations$r <- round(correlations$r, 1)
+  # Calculate new columns 'orbit_radius' and 'angle'
+  correlations <- transform(correlations,
+                            orbit_radius = 1 - round(abs(r), 1),
+                            angle = 2 * pi * seq_len(nrow(correlations)) / nrow(correlations)
+  )
+
+
+  # add correlation colour
+  correlations$colr <- ifelse(correlations$r <= 0, "blue", "red")
+  correlations <- na.omit(correlations)
+
+  # create animated plot
+  nframes <- num_frames
+  seqFrames <- (ncol(mat) - 1)
+
+  # ang <- rep(seq(0, 2 * pi, length.out = seqFrames), 10)
+  ang <- rep(seq(0, 2 * pi, length.out = nframes), seqFrames)
+  ang <- ang + rep(correlations$angle, each = nframes)
+
+  y <- x <- r <- id <- orbit_radius <- angle <- frame <- NULL
+  solar_system <- data.frame(
+    y = rep(correlations$y, each = nframes),
+    x = rep(correlations$x, each = nframes),
+    r = rep(correlations$r, each = nframes),
+    id = rep(correlations$id, each = nframes),
+    orbit_radius = rep(correlations$orbit_radius, each = nframes),
+    angle = ang,
+    colr = rep(correlations$colr, each = nframes),
+    frame = rep(1:nframes, seqFrames)
+  )
+
+
+  # Function to generate points along the circumference of a circle
+  circle_points <- function(radius, n_points = 100) {
+    data.frame(
+      x = radius * cos(seq(0, 2 * pi, length.out = n_points)),
+      y = radius * sin(seq(0, 2 * pi, length.out = n_points)),
+      r = radius
+    )
+  }
+
+  # Define a function to apply circle_points and assign an 'id' to each element in the list
+  create_circle_points_df <- function(radius, id) {
+    df <- circle_points(radius)
+    df$id <- id
+    return(df)
+  }
+
+  # Use lapply to apply the create_circle_points_df function to each unique orbit_radius
+  circle_data_list <- mapply(create_circle_points_df,
+                             unique(correlations$orbit_radius),
+                             seq_along(unique(correlations$orbit_radius)),
+                             SIMPLIFY = FALSE)
+
+  # Combine the resulting list of data frames into a single data frame using base R's 'do.call' and 'rbind'
+  circle_data <- do.call(rbind, circle_data_list)
+  circle_data$id <- as.character(circle_data$id)
+
+
+
+  # create df of circle names to display
+  circle_name <- data.frame(
+    nam = unique(round(abs(correlations$r), 1)),
+    nam2 = unique(round(abs(correlations$orbit_radius), 1))
+  )
+
+  suppressWarnings({
+    p <- ggplot() +
+      geom_path(data = circle_data, aes(x = x, y = y, group = id, color = id), linetype = "solid", alpha = 0.5) +
+      geom_point(data = solar_system, aes(
+        x = orbit_radius * cos(angle),
+        y = orbit_radius * sin(angle),
+        size = 3,
+        color = colr,
+        frame = frame,
+        label = r
+      ), alpha = 0.8) +
+      geom_text(data = solar_system, aes(
+        x = orbit_radius * cos(angle),
+        y = orbit_radius * sin(angle),
+        label = y,
+        frame = frame
+      ), hjust = -0.5, vjust = 0.5) +
+      geom_point(data = solar_system, aes(x = 0, y = 0), size = 6, color = "yellow") +
+      geom_text(data = solar_system, aes(x = 0, y = 0, label = sun), hjust = -0.5, vjust = -1) +
+      geom_text(
+        data = correlations, aes(x = 0, y = orbit_radius, label = round(abs(r), 1)),
+        size = 3.5, alpha = 0.3
+      ) +
+      coord_fixed() +
+      theme_void() +
+      theme(legend.position = "none") +
+      transition_manual(frame)
+  })
+
+  if (export) {
+    animation <- animate(p,
+      nframes = 500, fps = fps, end_pause = 0,
+      width = 800, height = 800, units = "px",
+      renderer = gifski_renderer()
+    )
+    anim_save(gif_name, animation, path = path)
+  } else {
+    ggplotly(p, tooltip = c("label"))
+  }
+}