Merge pull request #88 from UCD-SERG/visualization

Visualization

DESCRIPTION

@@ -1,10 +1,11 @@
 Package: serocalculator
 Type: Package
 Title: Estimating Infection Rates from Serological Data
-Version: 1.0.0
+Version: 1.0.0.9000
 Authors@R: c(
   person(given = "Peter", family = "Teunis", email = "[email protected]", role = c("aut", "cph"), comment = "Author of the method and original code."),
   person(given = "Kristina", family = "Lai", email = "[email protected]", role = c("aut", "cre")), 
+  person(given = "Chris", family = "Orwa", role = "aut"), 
   person(given = "Kristen", family = "Aiemjoy", email = "[email protected]", role = c("aut")),
   person(given = "Douglas Ezra", family = "Morrison", email = "[email protected]", role = c("aut")))
 Description: Translates antibody levels measured in cross-sectional population 
@@ -28,7 +29,9 @@ Imports:
     stats,
     tibble,
     tidyr,
-    utils
+    utils,
+    ggfortify,
+    cli
 Suggests:
     parallel,
     knitr,

NAMESPACE

@@ -69,6 +69,7 @@ importFrom(rngtools,RNGseq)
 importFrom(rngtools,setRNG)
 importFrom(stats,dlnorm)
 importFrom(stats,formula)
+importFrom(stats,lm)
 importFrom(stats,median)
 importFrom(stats,nlm)
 importFrom(stats,optim)

NEWS.md

@@ -1,3 +1,7 @@
+# serocalculator (development version)
+
+* Added `type = "age-scatter"` option for `autoplot.pop_data()`
+
 ## serocalculator 1.0.0
 
 * Moved underlying methods to `serocalculator` vignette

R/autoplot.pop_data.R

@@ -6,68 +6,117 @@
 #' @param log whether to show antibody responses on logarithmic scale
 #' @param strata the name of a variable in `pop_data` to stratify by (or `NULL` for no stratification)
 #' @param ... unused
+#' @param type an option to choose type of chart: the current options are `"density"` or `"age-scatter"`
 #'
 #' @return a [ggplot2::ggplot] object
-#' @export
+#'
 #' @examples
 #' library(dplyr)
 #' library(ggplot2)
+#' library(ggfortify)
 #'
 #' xs_data <- "https://osf.io/download//n6cp3/" %>%
-#' load_pop_data() %>%
-#' clean_pop_data()
-#'
-#' xs_data %>% autoplot(strata = "Country")
+#'   load_pop_data() %>%
+#'   clean_pop_data()
 #'
-autoplot.pop_data = function(
+#' xs_data %>% autoplot(strata = "Country", type = "density")
+#' xs_data %>% autoplot(strata = "Country", type = "age-scatter")
+#' @export
+autoplot.pop_data <- function(
     object,
-    log =  FALSE,
+    log = FALSE,
+    type = "density",
     strata = NULL,
-    ...)
-{
+    ...) {
+
+  if (type == "age-scatter") {
+    age_scatter(object, strata)
+  } else if (type == "density") {
+    density_plot(object, strata, log)
+  } else {
+    cli::cli_abort(
+      '`type = "{type}"` is not a valid input;
+      the currently available options for `type` are "density" or "age-scatter"')
+  }
+}
+
+age_scatter <- function(
+    object,
+    strata = NULL) {
+  # create default plotting
+
+  if(is.null(strata))
+  {
+    plot1 <-
+      object %>%
+      ggplot2::ggplot(aes(x = .data$age, y = .data$value))
+  } else
+  {
+    plot1 <-
+      object %>%
+      ggplot2::ggplot(aes(x = .data$age, y = .data$value, col = get(strata))) +
+      ggplot2::labs(colour = strata)
+  }
+
+  plot1 <- plot1 +
+    ggplot2::theme_linedraw() +
+    ggplot2::scale_y_log10() +
+    ggplot2::geom_point(size = .6, alpha = .7) +
+    ggplot2::geom_smooth(
+      method = "lm",
+      se = FALSE,
+      formula = y ~ x,
+      na.rm = TRUE) +
+    ggplot2::labs(
+      title = "Quantitative Antibody Responses by Age",
+      x = "Age",
+      y = "Antibody Response Value"
+    )
+
+  return(plot1)
+}
 
-  plot1 =
+# density plotting function
+density_plot <- function(
+    object,
+    strata = NULL,
+    log = FALSE) {
+  plot1 <-
     object %>%
     ggplot2::ggplot(aes(x = .data$value)) +
-    ggplot2::theme_minimal() +
+    ggplot2::theme_linedraw() +
     ggplot2::facet_wrap(~antigen_iso, nrow = 3)
 
-  if(!is.null(strata))
-  {
-    plot1 = plot1 +
+  if (is.null(strata)) {
+    plot1 <- plot1 +
       ggplot2::geom_density(
-        ggplot2::aes(fill = get(strata)),
         alpha = .6,
-        color = "black")
-  } else
-  {
-    plot1 = plot1 +
+        color = "black"
+      )
+  } else {
+    plot1 <- plot1 +
       ggplot2::geom_density(
-        # aes(fill = get(strata)),
         alpha = .6,
-        color = "black")
-}
-
-
-  if(log)
-  {
-    plot1 = plot1 +
+        color = "black",
+        aes(fill = get(strata))
+      ) +
+      ggplot2::labs(fill = strata)
+  }
+  if (log) {
+    plot1 <- plot1 +
       ggplot2::scale_x_log10() +
       ggplot2::labs(
         title = "Distribution of Cross-sectional Antibody Responses (Log transformed)",
         x = "Log10(Antibody Response Value)",
         y = "Frequency"
       )
-  } else
-  {
-    plot = plot1 +
+  } else {
+    plot1 <- plot1 +
       ggplot2::labs(
         title = "Distribution of Cross-sectional Antibody Responses",
         x = "Antibody Response Value",
         y = "Frequency"
       )
-
   }
-
   return(plot1)
-  }
+}

R/plot.seroincidence.est.R → R/autoplot.seroincidence.R

@@ -47,7 +47,8 @@ autoplot.seroincidence =
   {
     to_return = to_return +
       ggplot2::scale_x_log10(
-        labels = scales::label_comma())
+        labels = scales::label_comma()) +
+      ggplot2::theme_linedraw()
   }
 
   return(to_return)

R/plot.summary.seroincidence.by.R → R/autoplot.summary.seroincidence.by.R

@@ -53,7 +53,7 @@ autoplot.summary.seroincidence.by = function(
       alpha = alpha) +
     ggplot2::xlab(xvar) +
     ggplot2::ylab("Estimated incidence rate") +
-    ggplot2::theme_bw() +
+    ggplot2::theme_linedraw() +
     ggplot2::expand_limits(x = 0, y = 0) +
     ggplot2::labs(col = "`nlm()` convergence code") +
     ggplot2::theme(legend.position="bottom")

R/graph.decay.curves.R

@@ -43,12 +43,14 @@ plot_curve_params_one_ab = function(
       minor_breaks = NULL
     ) +
     # ggplot2::scale_x_log10() +
-    ggplot2::theme_minimal()  +
+    ggplot2::theme_linedraw()  +
     ggplot2::theme(
       axis.line = ggplot2::element_line()) +
     ggplot2::labs(
       x = "Days since fever onset",
-      y = "ELISA units")
+      y = "Antibody Concentration") +
+    ggplot2::ggtitle('Decay Curve') +
+    ggplot2::theme(plot.title = ggplot2::element_text(size = 20, face = "bold"))
 
   layer_function = function(cur_row)
   {

R/print.seroincidence.R

@@ -1,8 +1,8 @@
 #' @title
-#' Print Method for `seroincidence.by` Object
+#' Print Method for `seroincidence` Object
 #'
 #' @description
-#' Custom [print()] function to show output of the seroincidence calculator [est.incidence.by()].
+#' Custom [print()] function to show output of the seroincidence calculator [est.incidence()].
 #'
 #' @param x A list containing output of function [est.incidence.by()].
 #' @param ... Additional arguments affecting the summary produced.
@@ -21,17 +21,12 @@
 #' }
 #'
 #' @export
-print.seroincidence.by <- function(x, ...)
+print.seroincidence <- function(x, ...)
 {
-  cat("`seroincidence.by` object estimated given the following setup:\n")
-  cat(paste("a) Antigen isotypes   :", paste(attr(x, "antigen_isos"), collapse = ", ")), "\n")
-  cat(paste("b) Strata       :", paste(attr(x, "Strata") %>%  attr("strata_vars"), collapse = ", ")), "\n")
-
-    cat("\n")
-  cat("This object is a list of `seroincidence` objects, with added meta-data attributes:")
-  cat("`antigen_isos`   - Character vector of antigen isotypes used in analysis.\n")
-  cat("`Strata`       - Input parameter strata of function `est.incidence.by()`\n")
-  cat("\n")
+  cat("`seroincidence` object estimated given the following setup:\n")
+  cat(paste("a) `antigen_isos`: ", paste(attr(x, "antigen_isos"), collapse = ", ")), "\n")
+  cat(paste("b) `lambda_start`: ", attr(x, "lambda_start"), "\n"))
   cat("Call the `summary()` function to obtain output results.\n")
+  cat("Call the `autoplot()` function to graph the log-likelihood curve.\n")
   invisible(x)
 }

R/print.seroincidence.by.R

@@ -0,0 +1,37 @@
+#' @title
+#' Print Method for `seroincidence.by` Object
+#'
+#' @description
+#' Custom [print()] function to show output of the seroincidence calculator [est.incidence.by()].
+#'
+#' @param x A list containing output of function [est.incidence.by()].
+#' @param ... Additional arguments affecting the summary produced.
+#'
+#' @examples
+#'
+#' \dontrun{
+#' # estimate seroincidence
+#' seroincidence <- est.incidence.by(...)
+#'
+#' # print the seroincidence object to the console
+#' print(seroincidence)
+#'
+#' # or simply type (appropriate print method will be invoked automatically)
+#' seroincidence
+#' }
+#'
+#' @export
+print.seroincidence.by <- function(x, ...)
+{
+  cat("`seroincidence.by` object estimated given the following setup:\n")
+  cat(paste("a) Antigen isotypes   :", paste(attr(x, "antigen_isos"), collapse = ", ")), "\n")
+  cat(paste("b) Strata       :", paste(attr(x, "Strata") %>%  attr("strata_vars"), collapse = ", ")), "\n")
+
+    cat("\n")
+  cat("This object is a list of `seroincidence` objects, with added meta-data attributes:")
+  cat("`antigen_isos`   - Character vector of antigen isotypes used in analysis.\n")
+  cat("`Strata`       - Input parameter strata of function `est.incidence.by()`\n")
+  cat("\n")
+  cat("Call the `summary()` function to obtain output results.\n")
+  invisible(x)
+}

R/serocalculator-package.R

@@ -146,6 +146,7 @@
 #' @importFrom rngtools setRNG
 #' @importFrom stats dlnorm optim pgamma plnorm
 #' @importFrom stats formula
+#' @importFrom stats lm
 #' @importFrom stats median
 #' @importFrom stats nlm
 #' @importFrom stats qnorm