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#' Displays a longplot in a html file.
#'
#' A longplot is a range of suitable graphics that represent the relationship
#' within the values of one, or a limited number, of variables in a dataset. Each
#' graphic relates the values of all the selected variables and eventually the
#' row number in which they appear.
#'
#' In order to present the range of graphics, the user must define a dataset and
#' select at least one variable whitin it. Future work will include graphics that
#' can combine up to three variables.
#'
#' @seealso Specimens of grphics for \href{https://sciencegraph.github.io/brinton/articles/specimen.html}{univariate}
#' and \href{https://sciencegraph.github.io/brinton/articles/specimen2.html}{bivariate} data.
#'
#' @param data Data.frame. Default dataset to use for plot. If not already a
#' data.frame, it should be first coerced to by [as.data.frame()].
#' @param vars Character. A specific variable within the dataset.
#' @param label Logical. If `TRUE` the output includes labels that show the names
#' of the graphics that are being displayed.
#' @param dir Directory in which the files are stored.
#'
#' @return Cause the side-effect of creating and displaying a temporary html file
#' that includes a range of graphics suitable for this particular combination of
#' variables.
#' @export
#'
#' @examples
#' if (interactive()) {
#' longplot(esoph, "tobgp")
#' }
longplot <- function(data,
vars,
label = TRUE,
dir = tempdir()
)
{
# check markdown ----------------------------------------------------------
if (rmarkdown::pandoc_available("1.12.3") == FALSE) {print(warning_pandoc)}
else if (rmarkdown::pandoc_available("1.12.3") == TRUE) {
# aux functions -----------------------------------------------------------
# add_plots <- function(a, b) {
# write(
# paste0(
# "gridExtra::grid.arrange(",
# paste0(a, 1:b, collapse = ", "),
# ", ncol=5)"
# ),
# file.path(dir, "brinton_outcomes", "longplot.R"),
# append = TRUE
# )
# }
add_plots_patchwork <- function(a, b) {
write(
paste0(paste0(a, 1:b, collapse = " + "), " + patchwork::plot_layout(widths = rep(1, 5))"),
file.path(dir, "brinton_outcomes", "longplot.R"),
append = TRUE
)
}
add_plots_patchwork_guides <- function(a, b) {
write(
paste0(paste0(a, 1:b, collapse = " + "), " + patchwork::plot_spacer() + patchwork::plot_spacer() + patchwork::plot_layout(guides = 'collect', ncol = 5) & theme(legend.position = 'bottom', legend.key.size = unit(0.5,'line'), legend.title = element_blank()) & guides(position = 'bottom', fill = guide_legend(nrow = 1), color = guide_legend(nrow = 1))"),
file.path(dir, "brinton_outcomes", "longplot.R"),
append = TRUE
)
}
add_float_patchwork <- function(a, b, w, h, n) {
write(
paste0(paste0(a, 1:b, collapse = " + "), " + patchwork::plot_layout(widths = panel.", w,
", heights = panel.", h, ", ncol = ", n, ", )"),
file.path(dir, "brinton_outcomes", "longplot.R"),
append = TRUE
)
}
add_label <- function(a, b) {
char_types <-
paste0(a, " = c('", paste0(b, collapse = "', '"), "')")
write(
paste0('cat("', char_types, '")'),
file.path(dir, "brinton_outcomes", "longplot.R"),
append = TRUE
)
}
# check class -------------------------------------------------------------
if(is.data.frame(data) == FALSE) {
stop("I am so sorry, but this function only works with a data.frame input!\n",
"You have provided an object of class ", class(data))
}
if(tibble::is_tibble(data) == TRUE) {
# stop(warning_tibble)
data <- as.data.frame(data)
}
if(sum(as.vector(sapply(data, is.list) == TRUE)) > 0) {
data <- data[sapply(data, is.list) == F]
}
data_list <- lapply(data, FUN=remove_attr)
data <- as.data.frame(data_list)
string <- " argument expects a character vector"
if(is.character(vars) == FALSE) {
stop(paste0("The 'vars'", string))
}
# check vars --------------------------------------------------------------
if(length(vars) > 2) {
stop("Only 1 and 2 variables combinations have been considered.")
} else {
if (length(vars) == 1 & (
is.logical(unlist(data[, vars])) == TRUE |
is.factor(unlist(data[, vars])) == TRUE |
is.ordered(unlist(data[, vars])) == TRUE |
is.character(unlist(data[, vars])) == TRUE)
) {long <- length(unique(unlist(data[, vars])))/6 + 0.7}
else if (length(vars) == 1 & (
is.numeric(unlist(data[, vars])) == TRUE |
lubridate::is.instant(unlist(data[, vars])) == TRUE)
) {long <- 2}
else if (length(vars) == 2 & (
(lubridate::is.instant(unlist(data[, vars[1]])) == TRUE &
lubridate::is.instant(unlist(data[, vars[2]])) == TRUE) |
(is.numeric(unlist(data[, vars[1]])) == TRUE &
lubridate::is.instant(unlist(data[, vars[2]])) == TRUE) |
(lubridate::is.instant(unlist(data[, vars[1]])) == TRUE &
is.numeric(unlist(data[, vars[2]])) == TRUE))
) {long <- 2}
else if (length(vars) == 2 &
is.numeric(unlist(data[, vars[1]])) == TRUE &
is.numeric(unlist(data[, vars[2]])) == TRUE
) {long <- 2}
else if (length(vars) == 2 & ((
is.numeric(unlist(data[, vars[1]])) == TRUE &
is.factor(unlist(data[, vars[2]])) == TRUE) |
(
is.numeric(unlist(data[, vars[2]])) == TRUE &
is.factor(unlist(data[, vars[1]])) == TRUE))
) {long <- length(unlist(unique(data[, vars][which(sapply(data[, vars], is.factor))])))/4 + 0.5}
else if (length(vars) == 2 &
is.factor(unlist(data[, vars[1]])) == TRUE &
is.factor(unlist(data[, vars[2]])) == TRUE
) {wide <- length(unique(unlist(data[, vars[2]]))) / 5
long <- length(unique(unlist(data[, vars[2]]))) / 5
longt <- length(unique(unlist(data[, vars[1]]))) / 5}
else{stop("Only variables of the following classes have been considerated:
logical, Date, POSIXct, POSIXlt, numeric, factor, ord.factor and character. ")}
# setup -------------------------------------------------------------------
my_env <- new.env()
ncol <- 5
dir.create(file.path(dir, "brinton_outcomes", fsep = .Platform$file.sep), showWarnings = FALSE)
writeLines(output_long, file.path(dir, "brinton_outcomes", "longplot.R"))
write(paste0("cat('Graphics from the ",
deparse(substitute(vars)),
" variable(s) of the ",
sys.call()[2],
" dataframe')"),
file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
# 1var --------------------------------------------------------------------
# datetime ----------------------------------------------------------------
if (length(vars) == 1 & lubridate::is.instant(unlist(data[, vars])) == TRUE) {
write(paste0("#+ datetime, fig.width=12, fig.height=", long), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('line graph',
'stepped line graph')
dt11 <- pp_1DD_linegraph(data, colnames(data[vars]), pp_size = 1/ncol)
dt12 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol, pp_trans = 'step')
add_plots_patchwork("dt1", 2)
if (label == TRUE) {add_label("dtt", stripe)}
stripe <- c('point graph',
'point-to-point graph')
dt21 <- pp_1DD_pointgraph(data, colnames(data[vars]), pp_size = 1/ncol)
dt22 <- pp_1DD_linegraph(data, colnames(data[vars]), pp_size = 1/ncol, pp_points = TRUE)
add_plots_patchwork("dt2", 2)
if (label == TRUE) {add_label("dtt", stripe)}
stripe <- c('binned heatmap',
'bw binned heatmap',
'color binned heatmap')
dt31 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'black')
dt32 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'bw')
dt33 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'color')
add_plots_patchwork("dt3", 3)
if (label == TRUE) {add_label("dtt", stripe)}
stripe <- c('bw heatmap', 'color heatmap')
p151 <- pp_1DD_raster(data, colnames(data[vars]), 'yx', 'bw')
p152 <- pp_1DD_raster(data, colnames(data[vars]), 'yx', 'color')
add_plots_patchwork("p15", 2)
if (label == TRUE) {add_label("dtt", stripe)}
rmarkdown::render(file.path(dir, "brinton_outcomes", "longplot.R"),"html_document")
pander::openFileInOS(file.path(dir, "brinton_outcomes", "longplot.html"))}
# logical -----------------------------------------------------------------
else if (length(vars) == 1 & is.logical(unlist(data[, vars])) == TRUE) {
write(paste0("#+ logical, fig.width=12, fig.height=", long), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('line graph',
'point graph',
'point-to-point graph',
'tile plot',
'linerange graph')
lg11 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
lg12 <- pp_1DD_pointgraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
lg13 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol, pp_points = TRUE)
lg14 <- pp_1DD_tileplot(data, colnames(data[vars]), 'yx')
lg15 <- pp_1DD_linerange(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
add_plots_patchwork("lg1", 5)
if (label == TRUE) {add_label("lgc", stripe)}
stripe <- c('binned heatmap',
'bw binned heatmap',
'color binned heatmap')
lg21 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'black')
lg22 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'bw')
lg23 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'color')
add_plots_patchwork("lg2", 3)
if (label == TRUE) {add_label("lgc", stripe)}
stripe <- c('bar graph',
'bw bar graph',
'color bar graph')
lg31 <- pp_bargraph(data, colnames(data[vars]), 'black')
lg32 <- pp_bargraph(data, colnames(data[vars]), 'bw')
lg33 <- pp_bargraph(data, colnames(data[vars]), 'color')
add_plots_patchwork("lg3", 3)
if (label == TRUE) {add_label("lgc", stripe)}
rmarkdown::render(file.path(dir, "brinton_outcomes", "longplot.R"),"html_document")
pander::openFileInOS(file.path(dir, "brinton_outcomes", "longplot.html"))}
# ordered -----------------------------------------------------------------
else if (length(vars) == 1 & is.ordered(unlist(data[, vars])) == TRUE) {
# classes <- data[,vars]
# data[,vars] <- ifelse(nchar(as.vector(data[,vars])) > 10,
# paste0(substring(as.vector(data[,vars]), 1, 8), "..."), as.vector(data[,vars]))
# data[,vars] <- classes
write(paste0("#+ ordered, fig.width=12, fig.height=", long), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('line graph',
'point graph',
'point-to-point graph',
'tile plot',
'linerange graph')
of11 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
of12 <- pp_1DD_pointgraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
of13 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol, pp_points = TRUE)
of14 <- pp_1DD_tileplot(data, colnames(data[vars]), 'yx')
of15 <- pp_1DD_linerange(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
add_plots_patchwork("of1", 5)
if (label == TRUE) {add_label("ord", stripe)}
stripe <- c('binned heatmap',
'bw binned heatmap',
'color binned heatmap')
of21 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'black')
of22 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'bw')
of23 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'color')
add_plots_patchwork("of2", 3)
if (label == TRUE) {add_label("ord", stripe)}
stripe <- c('bar graph',
'bw bar graph',
'color bar graph')
of31 <- pp_bargraph(data, colnames(data[vars]), 'black')
of32 <- pp_bargraph(data, colnames(data[vars]), 'bw')
of33 <- pp_bargraph(data, colnames(data[vars]), 'color')
add_plots_patchwork("of3", 3)
if (label == TRUE) {add_label("ord", stripe)}
rmarkdown::render(file.path(dir, "brinton_outcomes", "longplot.R"),"html_document")
pander::openFileInOS(file.path(dir, "brinton_outcomes", "longplot.html"))}
# factor ------------------------------------------------------------------
else if (length(vars) == 1 & is.factor(unlist(data[, vars])) == TRUE & is.ordered(unlist(data[, vars])) == FALSE) {
# classes <- data[,vars]
# data[,vars] <- ifelse(nchar(as.vector(data[,vars])) > 10, paste0(substring(as.vector(data[,vars]), 1, 8), "..."), as.vector(data[,vars]))
# data[,vars] <- classes
write(paste0("#+ factor, fig.width=12, fig.height=", long), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
data[[vars]] <- factor(data[[vars]], levels = unique(data[[vars]]))
stripe <- c('line graph',
'point graph',
'point-to-point graph',
'tile plot',
'linerange graph')
ft11 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
ft12 <- pp_1DD_pointgraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
ft13 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol, pp_points = TRUE)
ft14 <- pp_1DD_tileplot(data, colnames(data[vars]), 'yx')
ft15 <- pp_1DD_linerange(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
add_plots_patchwork("ft1", 5)
if (label == TRUE) {add_label("fac", stripe)}
data[[vars]] <- forcats::fct_infreq(data[[vars]], ordered = TRUE)
stripe <- c('freq. reordered line graph',
'freq. reordered point graph',
'freq. reordered point-to-point graph',
'freq. reordered tile plot',
'freq. reordered linerange graph')
ft21 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
ft22 <- pp_1DD_pointgraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
ft23 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol, pp_points = TRUE)
ft24 <- pp_1DD_tileplot(data, colnames(data[vars]), 'yx')
ft25 <- pp_1DD_linerange(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
add_plots_patchwork("ft2", 5)
if (label == TRUE) {add_label("fac", stripe)}
data[[vars]] <- as.character(data[[vars]])
stripe <- c('alphab. reordered line graph',
'alphab. reordered point graph',
'alphab. reordered point-to-point graph',
'alphab. reordered tile plot',
'alphab. reordered linerange graph')
ft31 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
ft32 <- pp_1DD_pointgraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
ft33 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol, pp_points = TRUE)
ft34 <- pp_1DD_tileplot(data, colnames(data[vars]), 'yx')
ft35 <- pp_1DD_linerange(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
add_plots_patchwork("ft3", 5)
if (label == TRUE) {add_label("fac", stripe)}
data[[vars]] <- factor(data[[vars]], levels = unique(data[[vars]]))
stripe <- c('binned heatmap',
'bw binned heatmap',
'color binned heatmap')
ft41 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'black')
ft42 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'bw')
ft43 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'color')
add_plots_patchwork("ft4", 3)
if (label == TRUE) {add_label("fac", stripe)}
data[[vars]] <- forcats::fct_infreq(data[[vars]], ordered = TRUE)
stripe <- c('freq. reordered binned heatmap',
'bw freq. reordered binned heatmap',
'color freq. reordered binned heatmap')
ft51 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'black')
ft52 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'bw')
ft53 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'color')
add_plots_patchwork("ft5", 3)
if (label == TRUE) {add_label("fac", stripe)}
data[[vars]] <- as.character(data[[vars]])
stripe <- c('alphab. reordered binned heatmap',
'bw alphab. reordered binned heatmap',
'color alphab. reordered binned heatmap')
ft61 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'black')
ft62 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'bw')
ft63 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'color')
add_plots_patchwork("ft6", 3)
if (label == TRUE) {add_label("fac", stripe)}
data[[vars]] <- factor(data[[vars]], levels = unique(data[[vars]]))
stripe <- c('bar graph',
'bw bar graph',
'color bar graph')
ft71 <- pp_bargraph(data, colnames(data[vars]), 'black')
ft72 <- pp_bargraph(data, colnames(data[vars]), 'bw')
ft73 <- pp_bargraph(data, colnames(data[vars]), 'color')
add_plots_patchwork("ft7", 3)
if (label == TRUE) {add_label("fac", stripe)}
data[[vars]] <- forcats::fct_infreq(data[[vars]], ordered = TRUE)
stripe <- c('freq. reordered bar graph',
'bw freq. reordered bar graph',
'color freq. reordered bar graph')
ft81 <- pp_bargraph(data, colnames(data[vars]), 'black')
ft82 <- pp_bargraph(data, colnames(data[vars]), 'bw')
ft83 <- pp_bargraph(data, colnames(data[vars]), 'color')
add_plots_patchwork("ft8", 3)
if (label == TRUE) {add_label("fac", stripe)}
data[[vars]] <- as.character(data[[vars]])
stripe <- c('alphab. reordered bar graph',
'bw alphab. reordered bar graph',
'color alphab. reordered bar graph')
ft91 <- pp_bargraph(data, colnames(data[vars]), 'black')
ft92 <- pp_bargraph(data, colnames(data[vars]), 'bw')
ft93 <- pp_bargraph(data, colnames(data[vars]), 'color')
add_plots_patchwork("ft9", 3)
if (label == TRUE) {add_label("fac", stripe)}
rmarkdown::render(file.path(dir, "brinton_outcomes", "longplot.R"),"html_document")
pander::openFileInOS(file.path(dir, "brinton_outcomes", "longplot.html"))}
# character ---------------------------------------------------------------
else if (length(vars) == 1 & is.character(unlist(data[, vars])) == TRUE ) {
# data[,vars] <- ifelse(nchar(as.vector(data[,vars])) > 10, paste0(substring(as.vector(data[,vars]), 1, 8), "..."), as.vector(data[,vars]))
write(paste0("#+ character, fig.width=12, fig.height=", long), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
data[[vars]] <- factor(data[[vars]], levels = unique(data[[vars]]))
stripe <- c('line graph',
'point graph',
'point-to-point graph',
'tile plot',
'linerange graph')
p011 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
p012 <- pp_1DD_pointgraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
p013 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol, pp_points = TRUE)
p014 <- pp_1DD_tileplot(data, colnames(data[vars]), 'yx')
p015 <- pp_1DD_linerange(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
add_plots_patchwork("p01", 5)
if (label == TRUE) {add_label("cha", stripe)}
data[[vars]] <- forcats::fct_infreq(data[[vars]], ordered = TRUE)
stripe <- c('freq. reordered line graph',
'freq. reordered point graph',
'freq. reordered point-to-point graph',
'freq. reordered tile plot',
'freq. reordered linerange graph')
p021 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
p022 <- pp_1DD_pointgraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
p023 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol, pp_points = TRUE)
p024 <- pp_1DD_tileplot(data, colnames(data[vars]), 'yx')
p025 <- pp_1DD_linerange(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
add_plots_patchwork("p02", 5)
if (label == TRUE) {add_label("cha", stripe)}
data[[vars]] <- as.character(data[[vars]])
stripe <- c('alphab. reordered line graph',
'alphab. reordered point graph',
'alphab. reordered point-to-point graph',
'alphab. reordered tile plot',
'alphab. reordered linerange graph')
p031 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
p032 <- pp_1DD_pointgraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
p033 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol, pp_points = TRUE)
p034 <- pp_1DD_tileplot(data, colnames(data[vars]), 'yx')
p035 <- pp_1DD_linerange(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
add_plots_patchwork("p03", 5)
if (label == TRUE) {add_label("cha", stripe)}
data[[vars]] <- factor(data[[vars]], levels = unique(data[[vars]]))
stripe <- c('binned heatmap',
'bw binned heatmap',
'color binned heatmap')
p041 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'black')
p042 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'bw')
p043 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'color')
add_plots_patchwork("p04", 3)
if (label == TRUE) {add_label("cha", stripe)}
data[[vars]] <- forcats::fct_infreq(data[[vars]], ordered = TRUE)
stripe <- c('freq. reordered binned heatmap',
'bw freq. reordered binned heatmap',
'color freq. reordered binned heatmap')
p051 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'black')
p052 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'bw')
p053 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'color')
add_plots_patchwork("p05", 3)
if (label == TRUE) {add_label("cha", stripe)}
data[[vars]] <- as.character(data[[vars]])
stripe <- c('alphab. reordered binned heatmap',
'bw alphab. reordered binned heatmap',
'color alphab. reordered binned heatmap')
p061 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'black')
p062 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'bw')
p063 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'color')
add_plots_patchwork("p06", 3)
if (label == TRUE) {add_label("cha", stripe)}
data[[vars]] <- factor(data[[vars]], levels = unique(data[[vars]]))
stripe <- c('bar graph',
'bw bar graph',
'color bar graph')
p071 <- pp_bargraph(data, colnames(data[vars]), 'black')
p072 <- pp_bargraph(data, colnames(data[vars]), 'bw')
p073 <- pp_bargraph(data, colnames(data[vars]), 'color')
add_plots_patchwork("p07", 3)
if (label == TRUE) {add_label("cha", stripe)}
data[[vars]] <- forcats::fct_infreq(data[[vars]], ordered = TRUE)
stripe <- c('freq. reordered bar graph',
'bw freq. reordered bar graph',
'color freq. reordered bar graph')
p081 <- pp_bargraph(data, colnames(data[vars]), 'black')
p082 <- pp_bargraph(data, colnames(data[vars]), 'bw')
p083 <- pp_bargraph(data, colnames(data[vars]), 'color')
add_plots_patchwork("p08", 3)
if (label == TRUE) {add_label("cha", stripe)}
data[[vars]] <- as.character(data[[vars]])
stripe <- c('alphab. reordered bar graph',
'bw alphab. reordered bar graph',
'color alphab. reordered bar graph')
p091 <- pp_bargraph(data, colnames(data[vars]), 'black')
p092 <- pp_bargraph(data, colnames(data[vars]), 'bw')
p093 <- pp_bargraph(data, colnames(data[vars]), 'color')
add_plots_patchwork("p09", 3)
if (label == TRUE) {add_label("cha", stripe)}
rmarkdown::render(file.path(dir, "brinton_outcomes", "longplot.R"),"html_document")
pander::openFileInOS(file.path(dir, "brinton_outcomes", "longplot.html"))}
# numeric -----------------------------------------------------------------
else if (length(vars) == 1 & is.numeric(unlist(data[, vars])) == TRUE) {
my_binwidth <- (max(data[vars], na.rm=TRUE)-min(data[vars], na.rm=TRUE))/20
write(paste0("#+ numeric, fig.width=12, fig.height=", long), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('line graph',
'stepped line graph')
p011 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol)
p012 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol, pp_trans = 'step')
add_plots_patchwork("p01", 2)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('point-to-point graph',
'stepped point-to-point graph')
p161 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol, pp_points = TRUE)
p162 <- pp_1DD_linegraph(data, colnames(data[vars]), 'yx', pp_size = 1/ncol, pp_points = TRUE, pp_trans = 'step')
add_plots_patchwork("p16", 2)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('area graph')
p131 <- pp_1DD_areagraph(data, colnames(data[vars]), 'yx')
add_plots_patchwork("p13", 1)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('stepped area graph',
'bw stepped area graph',
'color stepped area graph')
p181 <- pp_1DD_areagraph(data, colnames(data[vars]), 'yx', pp_trans = 'step', pp_color = 'black')
p182 <- pp_1DD_areagraph(data, colnames(data[vars]), 'yx', pp_trans = 'step', pp_color = 'bw')
p183 <- pp_1DD_areagraph(data, colnames(data[vars]), 'yx', pp_trans = 'step', pp_color = 'color')
add_plots_patchwork("p18", 3)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('seq. stripe graph',
'bw seq. stripe graph',
'color seq. stripe graph')
p191 <- pp_1DD_stripegraph(data, colnames(data[vars]), pp_color = 'black')
p192 <- pp_1DD_stripegraph(data, colnames(data[vars]), pp_color = 'bw')
p193 <- pp_1DD_stripegraph(data, colnames(data[vars]), pp_color = 'color')
add_plots_patchwork("p19", 3)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('stripe graph', 'bw stripe graph', 'color stripe graph')
p021 <- pp_stripegraph(data, colnames(data[vars]), 'black')
p022 <- pp_stripegraph(data, colnames(data[vars]), 'bw')
p023 <- pp_stripegraph(data, colnames(data[vars]), 'color')
add_plots_patchwork("p02", 3)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('binned stripe graph',
'bw binned stripe graph',
'color binned stripe graph')
p031 <- pp_binned_stripegraph(data, colnames(data[vars]), 'black', my_binwidth)
p032 <- pp_binned_stripegraph(data, colnames(data[vars]), 'bw', my_binwidth)
p033 <- pp_binned_stripegraph(data, colnames(data[vars]), 'color', my_binwidth)
add_plots_patchwork("p03", 3)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('point graph',
'bw point graph',
'color point graph')
p041 <- pp_1DD_scatterplot(data, colnames(data[vars]), 'yx', pp_size = 3/ncol, 'black')
p042 <- pp_1DD_scatterplot(data, colnames(data[vars]), 'yx', pp_size = 3/ncol, 'bw')
p043 <- pp_1DD_scatterplot(data, colnames(data[vars]), 'yx', pp_size = 3/ncol, 'color')
add_plots_patchwork("p04", 3)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('point graph with trend line',
'bw point graph with trend line',
'color point graph with trend line')
p121 <- pp_1DD_scatterplot(data, colnames(data[vars]), 'yx', pp_size = 3/ncol, 'black', 'true')
p122 <- pp_1DD_scatterplot(data, colnames(data[vars]), 'yx', pp_size = 3/ncol, 'bw', 'true')
p123 <- pp_1DD_scatterplot(data, colnames(data[vars]), 'yx', pp_size = 3/ncol, 'color', 'true')
add_plots_patchwork("p12", 3)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('binned point graph',
'bw binned point graph',
'color binned point graph')
p051 <- pp_1DD_binnedpointgraph(data, colnames(data[vars]), 'yx', pp_size = 3/ncol, 'black')
p052 <- pp_1DD_binnedpointgraph(data, colnames(data[vars]), 'yx', pp_size = 3/ncol, 'bw')
p053 <- pp_1DD_binnedpointgraph(data, colnames(data[vars]), 'yx', pp_size = 3/ncol, 'color')
add_plots_patchwork("p05", 3)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('binned heatmap', 'bw binned heatmap', 'color binned heatmap')
p061 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'black')
p062 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'bw')
p063 <- pp_1DD_heatmap(data, colnames(data[vars]), 'yx', 'color')
add_plots_patchwork("p06", 3)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('blank', 'bw heatmap', 'color heatmap')
p151 <- blank(data, colnames(data[vars]))
p152 <- pp_1DD_raster(data, colnames(data[vars]), 'yx', 'bw')
p153 <- pp_1DD_raster(data, colnames(data[vars]), 'yx', 'color')
add_plots_patchwork("p15", 3)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('bar graph',
'bw bar graph',
'color bar graph')
p071 <- pp_bargraph(data, colnames(data[vars]), 'black', 'xy', pp_size = 0.2*my_binwidth)
p072 <- pp_bargraph(data, colnames(data[vars]), 'bw', 'xy', pp_size = 0.2*my_binwidth)
p073 <- pp_bargraph(data, colnames(data[vars]), 'color', 'xy', pp_size = 0.2*my_binwidth)
add_plots_patchwork("p07", 3)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('histogram',
'bw histogram',
'color histogram')
p081 <- pp_histogram(data, colnames(data[vars]), 'black', pp_binwidth = my_binwidth)
p082 <- pp_histogram(data, colnames(data[vars]), 'bw', pp_binwidth = my_binwidth)
p083 <- pp_histogram(data, colnames(data[vars]), 'color', pp_binwidth = my_binwidth)
add_plots_patchwork("p08", 3)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('freq. polygon')
p141 <- pp_histogram(data, colnames(data[vars]), 'black', 1, pp_geom = 'line', my_binwidth)
add_plots_patchwork("p14", 1)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('density plot',
'filled density plot')
p091 <- pp_density(data, colnames(data[vars]), pp_size = 1/ncol)
p092 <- pp_density(data, colnames(data[vars]), pp_size = 1/ncol, pp_color='black')
add_plots_patchwork("p09", 2)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('violin plot',
'filled violin plot')
p101 <- pp_violin(data, colnames(data[vars]), pp_size = 1/ncol)
p102 <- pp_violin(data, colnames(data[vars]), pp_size = 1/ncol, pp_color='black')
add_plots_patchwork("p10", 2)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('box plot',
'3 uniaxial',
'normal qq plot')
p111 <- pp_boxplot(data, colnames(data[vars]), pp_size = 1/ncol)
p112 <- pp_3uniaxial(data, colnames(data[vars]), pp_size = 4/ncol)
p113 <- qqplot(data, colnames(data[vars]), pp_size = 1/ncol)
add_plots_patchwork("p11", 3)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('ecfd plot',
'dotted ecfd plot',
'stepped ecfd plot')
p171 <- pp_ecdf(data, colnames(data[vars]), pp_trans = "rect")
p172 <- pp_ecdf(data, colnames(data[vars]), pp_trans = "point")
p173 <- pp_ecdf(data, colnames(data[vars]), pp_trans = "step")
add_plots_patchwork("p17", 3)
if (label == TRUE) {add_label("num", stripe)}
rmarkdown::render(file.path(dir, "brinton_outcomes", "longplot.R"),"html_document")
pander::openFileInOS(file.path(dir, "brinton_outcomes", "longplot.html"))
}
# 2var --------------------------------------------------------------------
# dtt~num -----------------------------------------------------------------
else if (length(vars) == 2 & (
(lubridate::is.instant(unlist(data[, vars[1]])) == TRUE &
lubridate::is.instant(unlist(data[, vars[2]])) == TRUE) |
(is.numeric(unlist(data[, vars[1]])) == TRUE &
lubridate::is.instant(unlist(data[, vars[2]])) == TRUE) |
(lubridate::is.instant(unlist(data[, vars[1]])) == TRUE &
is.numeric(unlist(data[, vars[2]])) == TRUE))) {
# my_binwidth <- (max(data[vars], na.rm=TRUE)-min(data[vars], na.rm=TRUE))/20
write(paste0("#+ numeric_datetime, fig.width=12, fig.height=", long), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('scatter plot', 'scatter plot with trend line')
p001 <- pp_scatterplot(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, pp_color = 'black', pp_smooth = FALSE)
p002 <- pp_scatterplot(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, pp_color = 'black', pp_smooth = TRUE)
add_plots_patchwork("p00", 2)
if (label == TRUE) {add_label("{dtt~num} OR {2dtt}", stripe)}
stripe <- c('binned scatter plot', 'bw binned scatter plot', 'color binned scatter plot')
p021 <- pp_binnedpointgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'black')
p022 <- pp_binnedpointgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'bw')
p023 <- pp_binnedpointgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'color')
add_plots_patchwork("p02", 3)
if (label == TRUE) {add_label("{dtt~num} OR {2dtt}", stripe)}
stripe <- c('binned heatmap', 'bw binned heatmap', 'color binned heatmap')
p031 <- pp_heatmap(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black')
p032 <- pp_heatmap(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw')
p033 <- pp_heatmap(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color')
add_plots_patchwork("p03", 3)
if (label == TRUE) {add_label("{dtt~num} OR {2dtt}", stripe)}
stripe <- c('blank', 'bw heatmap', 'color heatmap')
p051 <- blank2(data, colnames(data[vars][1]), colnames(data[vars][2]))
p052 <- pp_raster(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw')
p053 <- pp_raster(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color')
add_plots_patchwork("p05", 3)
if (label == TRUE) {add_label("{dtt~num} OR {2dtt}", stripe)}
stripe <- c('contour plot', 'bw contour plot', 'color contour plot')
p061 <- pp_contourmap(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'black')
p062 <- pp_contourmap(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'bw')
p063 <- pp_contourmap(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'color')
add_plots_patchwork("p06", 3)
if (label == TRUE) {add_label("{dtt~num} OR {2dtt}", stripe)}
stripe <- c('contour plot with data points')
p071 <- pp_contourmap(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black', pp_size = 3/ncol, 'TRUE')
add_plots_patchwork("p07", 1)
if (label == TRUE) {add_label("{dtt~num} OR {2dtt}", stripe)}
stripe <- c('path graph', 'bw path graph', 'color path graph')
p101 <- pp_pathgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), FALSE, 'black', pp_size = 3/ncol)
p102 <- pp_pathgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), FALSE, 'bw', pp_size = 3/ncol)
p103 <- pp_pathgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), FALSE, 'color', pp_size = 3/ncol)
add_plots_patchwork("p10", 3)
if (label == TRUE) {add_label("{dtt~num} OR {2dtt}", stripe)}
stripe <- c('point-to-point graph', 'bw point-to-point graph', 'color point-to-point graph')
p111 <- pp_pathgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), TRUE, 'black', pp_size = 3/ncol)
p112 <- pp_pathgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), TRUE, 'bw', pp_size = 3/ncol)
p113 <- pp_pathgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), TRUE, 'color', pp_size = 3/ncol)
add_plots_patchwork("p11", 3)
if (label == TRUE) {add_label("{dtt~num} OR {2dtt}", stripe)}
rmarkdown::render(file.path(dir, "brinton_outcomes", "longplot.R"),"html_document")
pander::openFileInOS(file.path(dir, "brinton_outcomes", "longplot.html"))
}
# 2num --------------------------------------------------------------------
else if (length(vars) == 2 & is.numeric(unlist(data[, vars[1]])) == TRUE & is.numeric(unlist(data[, vars[2]])) == TRUE) {
# my_binwidth <- (max(data[vars], na.rm=TRUE)-min(data[vars], na.rm=TRUE))/20
write(paste0("#+ numeric, fig.width=12, fig.height=", long), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('scatter plot', 'bw scatter plot', 'color scatter plot')
p001 <- pp_scatterplot(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'black', FALSE)
p002 <- pp_scatterplot(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'bw', FALSE)
p003 <- pp_scatterplot(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'color', FALSE)
add_plots_patchwork("p00", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('binned scatter plot', 'bw binned scatter plot', 'color binned scatter plot')
p021 <- pp_binnedpointgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'black')
p022 <- pp_binnedpointgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'bw')
p023 <- pp_binnedpointgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'color')
add_plots_patchwork("p02", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('binned heatmap', 'bw binned heatmap', 'color binned heatmap')
p031 <- pp_heatmap(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black')
p032 <- pp_heatmap(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw')
p033 <- pp_heatmap(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color')
add_plots_patchwork("p03", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('hexagonal binned heatmap', 'bw hexagonal binned heatmap', 'color hexagonal binned heatmap')
p041 <- pp_heatmap(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black', 6)
p042 <- pp_heatmap(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 6)
p043 <- pp_heatmap(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 6)
add_plots_patchwork("p04", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('blank', 'bw heatmap', 'color heatmap')
p051 <- blank2(data, colnames(data[vars][1]), colnames(data[vars][2]))
p052 <- pp_raster(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw')
p053 <- pp_raster(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color')
add_plots_patchwork("p05", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('contour plot', 'bw contour plot', 'color contour plot')
p061 <- pp_contourmap(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'black')
p062 <- pp_contourmap(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'bw')
p063 <- pp_contourmap(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'color')
add_plots_patchwork("p06", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('contour plot with data points', 'bw contour plot with data points', 'color contour plot with data points')
p071 <- pp_contourmap(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black', pp_size = 3/ncol, 'TRUE')
p072 <- pp_contourmap(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', pp_size = 3/ncol, 'TRUE')
p073 <- pp_contourmap(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', pp_size = 3/ncol, 'TRUE')
add_plots_patchwork("p07", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('scatter plot with confidence ellipse', 'bw scatter plot with confidence ellipse', 'color scatter plot with confidence ellipse')
p241 <- pp_scatterplot(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'black', FALSE, TRUE, FALSE)
p242 <- pp_scatterplot(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'bw', FALSE, TRUE, FALSE)
p243 <- pp_scatterplot(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'color', FALSE, TRUE, FALSE)
add_plots_patchwork("p24", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('scatter plot with marginal rugs', 'bw scatter plot with marginal rugs', 'color scatter plot with marginal rugs')
p251 <- pp_scatterplot(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'black', FALSE, FALSE, TRUE)
p252 <- pp_scatterplot(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'bw', FALSE, FALSE, TRUE)
p253 <- pp_scatterplot(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 3/ncol, 'color', FALSE, FALSE, TRUE)
add_plots_patchwork("p25", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('parallel plot', 'bw parallel plot', 'color parallel plot')
p081 <- pp_parallel(data, colnames(data[vars][1]), colnames(data[vars][2]), TRUE, 'black', pp_size = 3/ncol)
p082 <- pp_parallel(data, colnames(data[vars][1]), colnames(data[vars][2]), TRUE, 'bw', pp_size = 3/ncol)
p083 <- pp_parallel(data, colnames(data[vars][1]), colnames(data[vars][2]), TRUE, 'color', pp_size = 3/ncol)
add_plots_patchwork("p08", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('unscaled parallel plot', 'unscaled bw parallel plot', 'unscaled color parallel plot')
p091 <- pp_parallel(data, colnames(data[vars][1]), colnames(data[vars][2]), FALSE, 'black', pp_size = 3/ncol)
p092 <- pp_parallel(data, colnames(data[vars][1]), colnames(data[vars][2]), FALSE, 'bw', pp_size = 3/ncol)
p093 <- pp_parallel(data, colnames(data[vars][1]), colnames(data[vars][2]), FALSE, 'color', pp_size = 3/ncol)
add_plots_patchwork("p09", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('path graph', 'bw path graph', 'color path graph')
p101 <- pp_pathgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), FALSE, 'black', pp_size = 3/ncol)
p102 <- pp_pathgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), FALSE, 'bw', pp_size = 3/ncol)
p103 <- pp_pathgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), FALSE, 'color', pp_size = 3/ncol)
add_plots_patchwork("p10", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('point-to-point graph', 'bw point-to-point graph', 'color point-to-point graph')
p111 <- pp_pathgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), TRUE, 'black', pp_size = 3/ncol)
p112 <- pp_pathgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), TRUE, 'bw', pp_size = 3/ncol)
p113 <- pp_pathgraph(data, colnames(data[vars][1]), colnames(data[vars][2]), TRUE, 'color', pp_size = 3/ncol)
add_plots_patchwork("p11", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('point graph', 'bw point graph', 'color point graph')
p121 <- pp_unfolded(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black', pp_size = 3/ncol, pp_geom = 'point')
p122 <- pp_unfolded(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', pp_size = 3/ncol, pp_geom = 'point')
p123 <- pp_unfolded(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', pp_size = 3/ncol, pp_geom = 'point')
add_plots_patchwork("p12", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('line graph', 'stepped line graph')
p131 <- pp_unfolded(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black', pp_size = 3/ncol, pp_geom = 'line')
p132 <- pp_unfolded(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black', pp_size = 3/ncol, pp_geom = 'step')
add_plots_patchwork("p13", 2)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('area graph')
p141 <- pp_unfolded(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black', pp_size = 3/ncol, pp_geom = 'area')
add_plots_patchwork("p14", 1)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('stepped area graph', 'bw stepped area graph', 'color stepped area graph')
p151 <- pp_unfolded(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black', pp_size = 3/ncol, pp_geom = 'bar')
p152 <- pp_unfolded(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', pp_size = 3/ncol, pp_geom = 'bar')
p153 <- pp_unfolded(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', pp_size = 3/ncol, pp_geom = 'bar')
add_plots_patchwork("p15", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('blank', 'bw seq. heatmap', 'color seq. heatmap')
p161 <- blank2(data, colnames(data[vars][1]), colnames(data[vars][2]))
p162 <- pp_unf_raster(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', pp_size = 3/ncol, pp_geom = 'heat')
p163 <- pp_unf_raster(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', pp_size = 3/ncol, pp_geom = 'heat')
add_plots_patchwork("p16", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('blank', 'bw seq. stripe graph', 'color seq. stripe graph')
p171 <- blank2(data, colnames(data[vars][1]), colnames(data[vars][2]))
p172 <- pp_unf_tile(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', pp_size = 3/ncol, pp_geom = 'tile')
p173 <- pp_unf_tile(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', pp_size = 3/ncol, pp_geom = 'tile')
add_plots_patchwork("p17", 3)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('histogram', 'bw histogram', 'color histogram')
p181 <- pp_unf_yuxt(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black', pp_size = 3/ncol, pp_geom = 'hist')
p182 <- pp_unf_yuxt(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', pp_size = 3/ncol, pp_geom = 'hist')
p183 <- pp_unf_yuxt(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', pp_size = 3/ncol, pp_geom = 'hist')
add_plots_patchwork("p18", 3)
if (label == TRUE) {add_label("num", stripe)}
stripe <- c('freq. polygon')
p191 <- pp_unf_yuxt(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black', pp_size = 3/ncol, pp_geom = 'freq')
add_plots_patchwork("p19", 1)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('density plot', 'filled density plot')
p201 <- pp_unf_yuxt(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black', pp_size = 3/ncol, pp_geom = 'dens')
p202 <- pp_unf_yuxt(data, colnames(data[vars][1]), colnames(data[vars][2]), 'fill', pp_size = 3/ncol, pp_geom = 'dens')
add_plots_patchwork("p20", 2)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('violin plot', 'filled violin plot')
p211 <- pp_unf_yuxt(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black', pp_size = 3/ncol, pp_geom = 'viol')
p212 <- pp_unf_yuxt(data, colnames(data[vars][1]), colnames(data[vars][2]), 'fill', pp_size = 3/ncol, pp_geom = 'viol')
add_plots_patchwork("p21", 2)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('box plot')
p221 <- pp_unf_yuxt(data, colnames(data[vars][1]), colnames(data[vars][2]), 'black', pp_size = 3/ncol, pp_geom = 'box')
add_plots_patchwork("p22", 1)
if (label == TRUE) {add_label("2num", stripe)}
stripe <- c('ecdf plot', 'point ecdf plot', 'stepped ecdf plot')
p231 <- pp_unf_ecdf(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 1/ncol, pp_trans = 'line')
p232 <- pp_unf_ecdf(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 1/ncol, pp_trans = 'point')
p233 <- pp_unf_ecdf(data, colnames(data[vars][1]), colnames(data[vars][2]), pp_size = 1/ncol, pp_trans = 'step')
add_plots_patchwork("p23", 3)
if (label == TRUE) {add_label("2num", stripe)}
rmarkdown::render(file.path(dir, "brinton_outcomes", "longplot.R"),"html_document")
pander::openFileInOS(file.path(dir, "brinton_outcomes", "longplot.html"))
}
# ordnum ------------------------------------------------------------------
else if (length(vars) == 2 & ((
is.numeric(unlist(data[, vars[1]])) == TRUE &
is.ordered(unlist(data[, vars[2]])) == TRUE) |
(
is.numeric(unlist(data[, vars[2]])) == TRUE &
is.ordered(unlist(data[, vars[1]])) == TRUE))) {
write(paste0("#+ ordered_numeric, fig.width=12, fig.height=", long), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
var1 <- colnames(data[vars][which(sapply(data[vars], is.numeric))])
var2 <- colnames(data[vars][which(sapply(data[vars], is.ordered))])
stripe <- c('path graph',
'point graph',
'tile plot')
ordnum11 <- pp_basicgraph(data, var1, var2, pp_size = 1/ncol, 'line')
ordnum12 <- pp_basicgraph(data, var1, var2, pp_size = 1/ncol, 'point')
ordnum13 <- pp_basicgraph(data, var1, var2, pp_size = 1/ncol, 'tile')
add_plots_patchwork("ordnum1", 3)
if (label == TRUE) {add_label("ord-num", stripe)}
stripe <- c('binned heatmap',
'bw binned heatmap',
'color binned heatmap')
ordnum41 <- pp_basicgraph(data, var1, var2, pp_size = 1/ncol, 'bin', 'black')
ordnum42 <- pp_basicgraph(data, var1, var2, pp_size = 1/ncol, 'bin', 'bw')
ordnum43 <- pp_basicgraph(data, var1, var2, pp_size = 1/ncol, 'bin', 'color')
add_plots_patchwork("ordnum4", 3)
if (label == TRUE) {add_label("ord-num", stripe)}
stripe <- c('violin plot', 'filled violin plot')
ordnum21 <- pp_basicgraph(data, var2, var1, pp_size = 1/ncol, 'violin')
ordnum22 <- pp_basicgraph(data, var2, var1, pp_size = 1/ncol, 'violin filled')
add_plots_patchwork("ordnum2", 2)
if (label == TRUE) {add_label("ord-num", stripe)}
stripe <- c('box plot')
ordnum31 <- pp_basicgraph(data, var2, var1, pp_size = 1/ncol, 'box')
add_plots_patchwork("ordnum3", 1)
if (label == TRUE) {add_label("ord-num", stripe)}
write(paste0("#+ factor_numeric2, fig.width=12, fig.height=2.5"), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('blank',
'bw stacked histogram',
'color stacked histogram')
ordnum51 <- blank2(data, var1, var2)
ordnum52 <- pp_histogram2(data, var1, var2)
ordnum53 <- pp_histogram2(data, var1, var2, pp_color = "color", pp_scale = "ordinal")
add_plots_patchwork_guides("ordnum5", 3)
if (label == TRUE) {add_label("ord-num", stripe)}
stripe <- c('blank',
'bw 100% stacked histogram',
'color 100% stacked histogram')
ordnum61 <- blank2(data, var1, var2)
ordnum62 <- pp_histogram2(data, var1, var2, pp_position = "fill")
ordnum63 <- pp_histogram2(data, var1, var2, pp_color = "color", pp_position = "fill", pp_scale = "ordinal")
add_plots_patchwork_guides("ordnum6", 3)
if (label == TRUE) {add_label("ord-num", stripe)}
stripe <- c('density plot',
'bw density plot',
'color density plot')
ordnum71 <- pp_density2(data, var1, var2, 0.5, "line", "black")
ordnum72 <- pp_density2(data, var1, var2, 0.5, "line", "bw")
ordnum73 <- pp_density2(data, var1, var2, 0.5, "line", "viridis")
add_plots_patchwork_guides("ordnum7", 3)
if (label == TRUE) {add_label("ord-num", stripe)}
stripe <- c('blank',
'bw filled density plot',
'color filled density plot')
ordnum81 <- blank2(data, var1, var2)
ordnum82 <- pp_density2(data, var2, var1, 0.5, "area", "bw")
ordnum83 <- pp_density2(data, var2, var1, 0.5, "area", "viridis")
add_plots_patchwork_guides("ordnum8", 3)
if (label == TRUE) {add_label("ord-num", stripe)}
rmarkdown::render(file.path(dir, "brinton_outcomes", "longplot.R"),"html_document")
pander::openFileInOS(file.path(dir, "brinton_outcomes", "longplot.html"))
}
# facnum ------------------------------------------------------------------
else if (length(vars) == 2 & ((
is.numeric(unlist(data[, vars[1]])) == TRUE &
(is.factor(unlist(data[, vars[2]])) == TRUE & is.ordered(unlist(data[, vars[2]])) == FALSE)) |
(
is.numeric(unlist(data[, vars[2]])) == TRUE &
(is.factor(unlist(data[, vars[1]])) == TRUE & is.ordered(unlist(data[, vars[1]])) == FALSE)))) {
write(paste0("#+ factor_numeric, fig.width=12, fig.height=", long), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
var1 <- colnames(data[vars][which(sapply(data[vars], is.numeric))])
var2 <- colnames(data[vars][which(sapply(data[vars], is.factor))])
data2 <- data[ , c(var1, var2)]
data3b <- as.data.frame(stats::ftable(data2[2], useNA = "no"))
data2[,2] <- factor(data2[,2], levels = data3b[order(-data3b$Freq),][,1], ordered = TRUE)
data4 <- data[ , c(var1, var2)]
data4[,2] <- as.character(data4[,2])
stripe <- c('path graph',
'freq. reordered path graph',
'alphab. reordered path graph')
facnum011 <- pp_basicgraph(data, var1, var2, pp_size = 1/ncol, 'line')
facnum012 <- pp_basicgraph(data2, var1, var2, pp_size = 1/ncol, 'line')
facnum013 <- pp_basicgraph(data4, var1, var2, pp_size = 1/ncol, 'line')
add_plots_patchwork("facnum01", 3)
if (label == TRUE) {add_label("fac-num", stripe)}
stripe <- c('point graph',
'freq. reordered point graph',
'alphab. reordered point graph')
facnum021 <- pp_basicgraph(data, var1, var2, pp_size = 1/ncol, 'point')
facnum022 <- pp_basicgraph(data2, var1, var2, pp_size = 1/ncol, 'point')
facnum023 <- pp_basicgraph(data4, var1, var2, pp_size = 1/ncol, 'point')
add_plots_patchwork("facnum02", 3)
if (label == TRUE) {add_label("fac-num", stripe)}
stripe <- c('tile plot',
'freq. reordered tile plot',
'alphab. reordered tile plot')
facnum031 <- pp_basicgraph(data, var1, var2, pp_size = 1/ncol, 'tile')
facnum032 <- pp_basicgraph(data2, var1, var2, pp_size = 1/ncol, 'tile')
facnum033 <- pp_basicgraph(data4, var1, var2, pp_size = 1/ncol, 'tile')
add_plots_patchwork("facnum03", 3)
if (label == TRUE) {add_label("fac-num", stripe)}
stripe <- c('binned heatmap',
'freq. reordered binned heatmap',
'alphab. reordered binned heatmap')
facnum111 <- pp_basicgraph(data, var1, var2, pp_size = 1/ncol, 'bin', 'black')
facnum112 <- pp_basicgraph(data2, var1, var2, pp_size = 1/ncol, 'bin', 'black')
facnum113 <- pp_basicgraph(data4, var1, var2, pp_size = 1/ncol, 'bin', 'black')
add_plots_patchwork("facnum11", 3)
if (label == TRUE) {add_label("fac-num", stripe)}
stripe <- c('bw binned heatmap',
'bw freq. reordered binned heatmap',
'bw alphab. reordered binned heatmap')
facnum121 <- pp_basicgraph(data, var1, var2, pp_size = 1/ncol, 'bin', 'bw')
facnum122 <- pp_basicgraph(data2, var1, var2, pp_size = 1/ncol, 'bin', 'bw')
facnum123 <- pp_basicgraph(data4, var1, var2, pp_size = 1/ncol, 'bin', 'bw')
add_plots_patchwork("facnum12", 3)
if (label == TRUE) {add_label("fac-num", stripe)}
stripe <- c('color binned heatmap',
'color freq. reordered binned heatmap',
'color alphab. reordered binned heatmap')
facnum131 <- pp_basicgraph(data, var1, var2, pp_size = 1/ncol, 'bin', 'color')
facnum132 <- pp_basicgraph(data2, var1, var2, pp_size = 1/ncol, 'bin', 'color')
facnum133 <- pp_basicgraph(data4, var1, var2, pp_size = 1/ncol, 'bin', 'color')
add_plots_patchwork("facnum13", 3)
if (label == TRUE) {add_label("fac-num", stripe)}
stripe <- c('violin plot', 'freq. reordered violin plot', 'alphab. reordered violin plot')
facnum211 <- pp_basicgraph(data, var2, var1, pp_size = 1/ncol, 'violin')
facnum212 <- pp_basicgraph(data2, var2, var1, pp_size = 1/ncol, 'violin')
facnum213 <- pp_basicgraph(data4, var2, var1, pp_size = 1/ncol, 'violin')
add_plots_patchwork("facnum21", 3)
if (label == TRUE) {add_label("fac-num", stripe)}
stripe <- c('filled violin plot', 'freq. reordered filled violin plot', 'alphab. reordered filled violin plot')
facnum221 <- pp_basicgraph(data, var2, var1, pp_size = 1/ncol, 'violin filled')
facnum222 <- pp_basicgraph(data2, var2, var1, pp_size = 1/ncol, 'violin filled')
facnum223 <- pp_basicgraph(data4, var2, var1, pp_size = 1/ncol, 'violin filled')
add_plots_patchwork("facnum22", 3)
if (label == TRUE) {add_label("fac-num", stripe)}
stripe <- c('box plot', 'freq. reordered box plot', 'alphab. reordered box plot')
facnum311 <- pp_basicgraph(data, var2, var1, pp_size = 1/ncol, 'box')
facnum312 <- pp_basicgraph(data2, var2, var1, pp_size = 1/ncol, 'box')
facnum313 <- pp_basicgraph(data4, var2, var1, pp_size = 1/ncol, 'box')
add_plots_patchwork("facnum31", 3)
if (label == TRUE) {add_label("fac-num", stripe)}
write(paste0("#+ factor_numeric2, fig.width=12, fig.height=2.5"), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('blank',
'bw stacked histogram',
'color stacked histogram')
facnum51 <- blank2(data, var1, var2)
facnum52 <- pp_histogram2(data, var1, var2)
facnum53 <- pp_histogram2(data, var1, var2, pp_color = "color")
add_plots_patchwork_guides("facnum5", 3)
if (label == TRUE) {add_label("fac-num", stripe)}
stripe <- c('blank',
'bw 100% stacked histogram',
'color 100% stacked histogram')
facnum61 <- blank2(data, var1, var2)
facnum62 <- pp_histogram2(data, var1, var2, pp_position = "fill")
facnum63 <- pp_histogram2(data, var1, var2, pp_color = "color", pp_position = "fill")
add_plots_patchwork_guides("facnum6", 3)
if (label == TRUE) {add_label("fac-num", stripe)}
stripe <- c('density plot',
'blank',
'color density plot')
facnum71 <- pp_density2(data, var1, var2, 0.5, "line", "black")
facnum72 <- blank2(data, var1, var2)
facnum73 <- pp_density2(data, var1, var2, 0.5, "line", "color")
add_plots_patchwork_guides("facnum7", 3)
if (label == TRUE) {add_label("fac-num", stripe)}
stripe <- c('blank',
'filled density plot',
'color filled density plot')
facnum81 <- blank2(data, var1, var2)
facnum82 <- pp_density2(data, var2, var1, 0.5, "area", "bw")
facnum83 <- pp_density2(data, var2, var1, 0.5, "area", "color")
add_plots_patchwork_guides("facnum8", 3)
if (label == TRUE) {add_label("fac-num", stripe)}
rmarkdown::render(file.path(dir, "brinton_outcomes", "longplot.R"),"html_document")
pander::openFileInOS(file.path(dir, "brinton_outcomes", "longplot.html"))
}
# 2ord --------------------------------------------------------------------
else if (length(vars) == 2 & is.ordered(unlist(data[, vars[1]])) == TRUE & is.ordered(unlist(data[, vars[2]])) == TRUE) {
panel.h <- unit(nrow(unique(data[vars[1]]))*0.7, "cm")
panel.w <- unit(3.5, "cm")
panel.h2 <- unit(nrow(unique(data[vars[2]]))*0.7, "cm")
panel.w2 <- unit(nrow(unique(data[vars[1]]))*0.7, "cm")
write(paste0("#+ 2ord_1, fig.width=8, fig.height=", long+1), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('bw stacked bar graph', 'color stacked bar graph')
ofof01 <- pp_stackedbar(data, colnames(data[vars][2]), colnames(data[vars][1]), 'bw', 'stack', 'ordinal')
ofof02 <- pp_stackedbar(data, colnames(data[vars][2]), colnames(data[vars][1]), 'color', 'stack', 'ordinal')
add_float_patchwork("ofof0", 2, "w", "h2", 2)
if (label == TRUE) {add_label("2ord", stripe)}
write(paste0("#+ 2ord_2, fig.width=8, fig.height=", longt+1), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('transposed bw stacked bar graph', 'transposed color stacked bar graph')
ofof051 <- pp_stackedbar(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'stack', 'ordinal')
ofof052 <- pp_stackedbar(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'stack', 'ordinal')
add_float_patchwork("ofof05", 2, "w", "h", 2)
if (label == TRUE) {add_label("2ord", stripe)}
write(paste0("#+ 2ord_3, fig.width=8, fig.height=", long+1), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('bw 100% stacked bar graph', 'color 100% stacked bar graph')
ofof11 <- pp_stackedbar(data, colnames(data[vars][2]), colnames(data[vars][1]), 'bw', 'fill', 'ordinal')
ofof12 <- pp_stackedbar(data, colnames(data[vars][2]), colnames(data[vars][1]), 'color', 'fill', 'ordinal')
add_float_patchwork("ofof1", 2, "w", "h2", 2)
if (label == TRUE) {add_label("2ord", stripe)}
write(paste0("#+ 2ord_4, fig.width=8, fig.height=", longt+1), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('transposed bw 100% stacked bar graph', 'transposed color 100% stacked bar graph')
ofof151 <- pp_stackedbar(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'fill', 'ordinal')
ofof152 <- pp_stackedbar(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'fill', 'ordinal')
add_float_patchwork("ofof15", 2, "w", "h", 2)
if (label == TRUE) {add_label("2ord", stripe)}
write(paste0("#+ 2ord_5, fig.width=", longt*2+5, ", fig.height=", long+1.5), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('bw heatmap', 'color heatmap')
ofof21 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'observed')
ofof22 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'observed')
add_float_patchwork("ofof2", 2, "w2", "h2", 2)
if (label == TRUE) {add_label("2ord", stripe)}
stripe <- c('blank', 'color residuals heatmap')
ofof41 <- blank2(data, colnames(data[vars][1]), colnames(data[vars][2]))
ofof42 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'residuals')
add_float_patchwork("ofof4", 2, "w2", "h2", 2)
if (label == TRUE) {add_label("2ord", stripe)}
stripe <- c('bw contribution to x2 heatmap', 'color contribution to x2 heatmap')
ofof61 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'contrib')
ofof62 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'contrib')
add_float_patchwork("ofof6", 2, "w2", "h2", 2)
if (label == TRUE) {add_label("2ord", stripe)}
stripe <- c('bw balloon plot', 'color balloon plot')
ofof101 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'observed', pp_geom = 'point')
ofof102 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'observed', pp_geom = 'point')
add_float_patchwork("ofof10", 2, "w2", "h2", 2)
if (label == TRUE) {add_label("2ord", stripe)}
stripe <- c('blank', 'color residuals balloon plot')
ofof121 <- blank2(data, colnames(data[vars][1]), colnames(data[vars][2]))
ofof122 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'residuals', pp_geom = 'point')
add_float_patchwork("ofof12", 2, "w2", "h2", 2)
if (label == TRUE) {add_label("2ord", stripe)}
stripe <- c('bw contribution to x2 balloon plot', 'color contribution to x2 balloon plot')
ofof141 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'contrib', pp_geom = 'point')
ofof142 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'contrib', pp_geom = 'point')
add_float_patchwork("ofof14", 2, "w2", "h2", 2)
if (label == TRUE) {add_label("2ord", stripe)}
rmarkdown::render(file.path(dir, "brinton_outcomes", "longplot.R"),"html_document")
pander::openFileInOS(file.path(dir, "brinton_outcomes", "longplot.html"))
}
# 2fac --------------------------------------------------------------------
else if (length(vars) == 2 &
(is.factor(unlist(data[, vars[1]])) == TRUE & is.ordered(unlist(data[, vars[1]])) == FALSE) &
(is.factor(unlist(data[, vars[2]])) == TRUE & is.ordered(unlist(data[, vars[2]])) == FALSE)) {
panel.h <- unit(nrow(unique(data[vars[1]]))*0.7, "cm")
panel.h2 <- unit(nrow(unique(data[vars[2]]))*0.7, "cm")
panel.w <- unit(3.5, "cm")
data2 <- data[, vars]
data3 <- as.data.frame(stats::ftable(data2[1], useNA = "no"))
data3b <- as.data.frame(stats::ftable(data2[2], useNA = "no"))
data2[,1] <- factor(data2[,1], levels = data3[order(-data3$Freq),][,1], ordered = TRUE)
data2[,2] <- factor(data2[,2], levels = data3b[order(-data3b$Freq),][,1], ordered = TRUE)
data4 <- data[, vars]
data4[[vars[1]]] <- as.character(data4[[vars[1]]])
data4[[vars[2]]] <- as.character(data4[[vars[2]]])
write(paste0("#+ 2fac_1, fig.width=12, fig.height=", long+1), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('color stacked bar graph', 'color freq. reordered stacked bar graph', 'color alphab. reordered stacked bar graph')
fafa01 <- pp_stackedbar(data, colnames(data2[vars][2]), colnames(data2[vars][1]), 'color', 'stack')
fafa02 <- pp_stackedbar(data2, colnames(data2[vars][2]), colnames(data2[vars][1]), 'color', 'stack')
fafa03 <- pp_stackedbar(data4, colnames(data4[vars][2]), colnames(data4[vars][1]), 'color', 'stack')
add_float_patchwork("fafa0", 3, "w", "h2", 3)
if (label == TRUE) {add_label("2fac", stripe)}
write(paste0("#+ 2fac_2, fig.width=12, fig.height=", longt+1), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('transposed color stacked bar graph', 'transposed color freq. reordered stacked bar graph', 'transposed color alphab. reordered stacked bar graph')
fafa051 <- pp_stackedbar(data, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'stack')
fafa052 <- pp_stackedbar(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'stack')
fafa053 <- pp_stackedbar(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'stack')
add_float_patchwork("fafa05", 3, "w", "h", 3)
if (label == TRUE) {add_label("2fac", stripe)}
write(paste0("#+ 2fac_3, fig.width=12, fig.height=", long+1), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('color 100% stacked bar graph', 'color freq. reordered 100% stacked bar graph', 'color alphab. reordered 100% stacked bar graph')
fafa11 <- pp_stackedbar(data, colnames(data[vars][2]), colnames(data[vars][1]), 'color', 'fill')
fafa12 <- pp_stackedbar(data2, colnames(data2[vars][2]), colnames(data2[vars][1]), 'color', 'fill')
fafa13 <- pp_stackedbar(data4, colnames(data4[vars][2]), colnames(data4[vars][1]), 'color', 'fill')
add_float_patchwork("fafa1", 3, "w", "h2", 3)
if (label == TRUE) {add_label("2fac", stripe)}
write(paste0("#+ 2fac_4, fig.width=12, fig.height=", longt+1), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('transposed color 100% stacked bar graph', 'transposed color freq. reordered 100% stacked bar graph', 'transposed color alphab. reordered 100% stacked bar graph')
fafa151 <- pp_stackedbar(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'fill')
fafa152 <- pp_stackedbar(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'fill')
fafa153 <- pp_stackedbar(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'fill')
add_float_patchwork("fafa15", 3, "w", "h", 3)
if (label == TRUE) {add_label("2fac", stripe)}
panel.h2 <- unit(nrow(unique(data[vars[2]]))*0.7, "cm")
panel.w2 <- unit(nrow(unique(data[vars[1]]))*0.7, "cm")
write(paste0("#+ 2fac_5, fig.width=", wide*3+10, ", fig.height=", long+1.5), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('bw heatmap', 'bw freq. reordered heatmap', 'bw alphab. reordered heatmap')
fafa21 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'observed')
fafa22 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'bw', 'observed')
fafa23 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'bw', 'observed')
add_float_patchwork("fafa2", 3, "w2", "h2", 3)
if (label == TRUE) {add_label("2fac", stripe)}
stripe <- c('color heatmap', 'color freq. reordered heatmap', 'color alphab. reordered heatmap')
fafa31 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'observed')
fafa32 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'observed')
fafa33 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'observed')
add_float_patchwork("fafa3", 3, "w2", "h2", 3)
if (label == TRUE) {add_label("2fac", stripe)}
stripe <- c('color residuals heatmap', 'color freq. reordered residuals heatmap', 'color alphab. reordered residuals heatmap')
fafa41 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'residuals')
fafa42 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'residuals')
fafa43 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'residuals')
add_float_patchwork("fafa4", 3, "w2", "h2", 3)
if (label == TRUE) {add_label("2fac", stripe)}
stripe <- c('bw contribution to x2 heatmap', 'bw freq. reordered contribution to x2 heatmap', 'bw alphab. reordered contribution to x2 heatmap')
fafa61 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'contrib')
fafa62 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'bw', 'contrib')
fafa63 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'bw', 'contrib')
add_float_patchwork("fafa6", 3, "w2", "h2", 3)
if (label == TRUE) {add_label("2fac", stripe)}
stripe <- c('color contribution to x2 heatmap', 'color freq. reordered contribution to x2 heatmap', 'color alphab. reordered contribution to x2 heatmap')
fafa71 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'contrib')
fafa72 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'contrib')
fafa73 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'contrib')
add_float_patchwork("fafa7", 3, "w2", "h2", 3)
if (label == TRUE) {add_label("2fac", stripe)}
stripe <- c('bw balloon plot', 'bw freq. reordered balloon plot', 'bw alphab. reordered balloon plot')
fafa81 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'observed', pp_geom = "point")
fafa82 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'bw', 'observed', pp_geom = "point")
fafa83 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'bw', 'observed', pp_geom = "point")
add_float_patchwork("fafa8", 3, "w2", "h2", 3)
if (label == TRUE) {add_label("2fac", stripe)}
stripe <- c('color balloon plot', 'color freq. reordered balloon plot', 'color alphab. reordered balloon plot')
fafa91 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'observed', pp_geom = "point")
fafa92 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'observed', pp_geom = "point")
fafa93 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'observed', pp_geom = "point")
add_float_patchwork("fafa9", 3, "w2", "h2", 3)
if (label == TRUE) {add_label("2fac", stripe)}
stripe <- c('color residuals balloon plot', 'color freq. reordered residuals balloon plot', 'color alphab. reordered residuals balloon plot')
fafa101 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'residuals', pp_geom = "point")
fafa102 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'residuals', pp_geom = "point")
fafa103 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'residuals', pp_geom = "point")
add_float_patchwork("fafa10", 3, "w2", "h2", 3)
if (label == TRUE) {add_label("2fac", stripe)}
stripe <- c('bw contribution to x2 balloon plot', 'bw freq. reordered contribution to x2 balloon plot', 'bw alphab. reordered contribution to x2 balloon plot')
fafa121 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'contrib', pp_geom = "point")
fafa122 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'bw', 'contrib', pp_geom = "point")
fafa123 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'bw', 'contrib', pp_geom = "point")
add_float_patchwork("fafa12", 3, "w2", "h2", 3)
if (label == TRUE) {add_label("2fac", stripe)}
stripe <- c('color contribution to x2 balloon plot', 'color freq. reordered contribution to x2 balloon plot', 'color alphab. reordered contribution to x2 balloon plot')
fafa131 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'contrib', pp_geom = "point")
fafa132 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'contrib', pp_geom = "point")
fafa133 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'contrib', pp_geom = "point")
add_float_patchwork("fafa13", 3, "w2", "h2", 3)
if (label == TRUE) {add_label("2fac", stripe)}
rmarkdown::render(file.path(dir, "brinton_outcomes", "longplot.R"),"html_document")
pander::openFileInOS(file.path(dir, "brinton_outcomes", "longplot.html"))
}
# facord ------------------------------------------------------------------
else if (length(vars) == 2 &
((
is.ordered(unlist(data[, vars[1]])) == TRUE &
(is.factor(unlist(data[, vars[2]])) == TRUE & is.ordered(unlist(data[, vars[2]])) == FALSE)) |
(
is.ordered(unlist(data[, vars[2]])) == TRUE &
(is.factor(unlist(data[, vars[1]])) == TRUE & is.ordered(unlist(data[, vars[1]])) == FALSE)))) {
var2 <- colnames(data[vars][,sapply(data[vars], function(x) is.factor(x) & !is.ordered(x)), drop = FALSE])
var1 <- colnames(data[vars][which(sapply(data[vars], is.ordered))])
panel.h <- unit(length(unique(data[,var2]))*0.7, "cm")
panel.h2 <- unit(length(unique(data[,var1]))*0.7, "cm")
panel.w <- unit(3.5, "cm")
data2 <- data[, vars]
data3b <- as.data.frame(stats::ftable(data2[2], useNA = "no"))
data2[,2] <- factor(data2[,2], levels = data3b[order(-data3b$Freq),][,1], ordered = TRUE)
data4 <- data[, vars]
data4[[vars[2]]] <- as.character(data4[[vars[2]]])
write(paste0("#+ facord_1, fig.width=12, fig.height=", length(unique(unlist(data[, var2]))) / 3.7 + 1), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('bw stacked bar graph', 'bw freq. reordered stacked bar graph', 'bw alphab. reordered stacked bar graph')
offa01 <- pp_stackedbar(data, var2, var1, 'bw', 'stack')
offa02 <- pp_stackedbar(data2, var2, var1, 'bw', 'stack')
offa03 <- pp_stackedbar(data4, var2, var1, 'bw', 'stack')
add_float_patchwork("offa0", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
stripe <- c('color stacked bar graph', 'color freq. reordered stacked bar graph', 'color alphab. reordered stacked bar graph')
offa11 <- pp_stackedbar(data, var2, var1, 'color', 'stack', 'ordinal')
offa12 <- pp_stackedbar(data2, var2, var1, 'color', 'stack', 'ordinal')
offa13 <- pp_stackedbar(data4, var2, var1, 'color', 'stack', 'ordinal')
add_float_patchwork("offa1", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
write(paste0("#+ facord_2, fig.width=12, fig.height=", length(unique(unlist(data[, var1]))) / 3.7 + 1), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('transposed color stacked bar graph')
offa211 <- pp_stackedbar(data, var1, var2, 'color', 'stack')
add_float_patchwork("offa21", 1, "w", "h2", 3)
if (label == TRUE) {add_label("offa", stripe)}
write(paste0("#+ facord_3, fig.width=12, fig.height=", length(unique(unlist(data[, var2]))) / 3.7 + 1), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('bw 100% stacked bar graph', 'bw freq. reordered 100% stacked bar graph', 'bw alphab. reordered 100% stacked bar graph')
offa21 <- pp_stackedbar(data, var2, var1, pp_color = 'bw', pp_position = 'fill')
offa22 <- pp_stackedbar(data2, var2, var1, pp_color = 'bw', pp_position = 'fill')
offa23 <- pp_stackedbar(data4, var2, var1, pp_color = 'bw', pp_position = 'fill')
add_float_patchwork("offa2", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
stripe <- c('color 100% stacked bar graph', 'color freq. reordered 100% stacked bar graph', 'color alphab. reordered 100% stacked bar graph')
offa31 <- pp_stackedbar(data, var2, var1, pp_color = 'color', pp_position = 'fill', 'ordinal')
offa32 <- pp_stackedbar(data2, var2, var1, pp_color = 'color', pp_position = 'fill', 'ordinal')
offa33 <- pp_stackedbar(data4, var2, var1, pp_color = 'color', pp_position = 'fill', 'ordinal')
add_float_patchwork("offa3", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
write(paste0("#+ facord_4, fig.width=12, fig.height=", length(unique(unlist(data[, var1]))) / 3.7 + 1), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
stripe <- c('transposed color 100% stacked bar graph')
offa221 <- pp_stackedbar(data, var1, var2, 'color', 'fill')
add_float_patchwork("offa22", 1, "w", "h2", 3)
if (label == TRUE) {add_label("offa", stripe)}
write(paste0("#+ facord_5, fig.width=12, fig.height=", length(unique(unlist(data[, var2]))) / 3.7 + 1.5), file.path(dir, "brinton_outcomes", "longplot.R"), append=TRUE)
panel.w2 <- unit(nrow(unique(data[vars[1]]))*0.7, "cm")
stripe <- c('bw heatmap', 'bw freq. reordered heatmap', 'bw alphab. reordered heatmap')
offa41 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'observed')
offa42 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'bw', 'observed')
offa43 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'bw', 'observed')
add_float_patchwork("offa4", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
stripe <- c('color heatmap', 'color freq. reordered heatmap', 'color alphab. reordered heatmap')
offa51 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'observed')
offa52 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'observed')
offa53 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'observed')
add_float_patchwork("offa5", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
stripe <- c('color residuals heatmap', 'color freq. reordered residuals heatmap', 'color alphab. reordered residuals heatmap')
offa61 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'residuals')
offa62 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'residuals')
offa63 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'residuals')
add_float_patchwork("offa6", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
stripe <- c('bw contribution to x2 heatmap', 'color contribution to x2 heatmap')
offa81 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'contrib')
offa82 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'bw', 'contrib')
offa83 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'bw', 'contrib')
add_float_patchwork("offa8", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
stripe <- c('bw freq. reordered contribution to x2 heatmap', 'color freq. reordered contribution to x2 heatmap')
offa91 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'contrib')
offa92 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'contrib')
offa93 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'contrib')
add_float_patchwork("offa9", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
stripe <- c('bw balloon plot', 'bw freq. reordered balloon plot', 'bw alphab. reordered balloon plot')
offa101 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'observed', pp_geom = "point")
offa102 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'bw', 'observed', pp_geom = "point")
offa103 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'bw', 'observed', pp_geom = "point")
add_float_patchwork("offa10", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
stripe <- c('color balloon plot', 'color freq. reordered balloon plot', 'color alphab. reordered balloon plot')
offa111 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'observed', pp_geom = "point")
offa112 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'observed', pp_geom = "point")
offa113 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'observed', pp_geom = "point")
add_float_patchwork("offa11", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
stripe <- c('color residuals balloon plot', 'color freq. reordered residuals balloon plot', 'color alphab. reordered residuals balloon plot')
offa121 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'residuals', pp_geom = "point")
offa122 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'residuals', pp_geom = "point")
offa123 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'residuals', pp_geom = "point")
add_float_patchwork("offa12", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
stripe <- c('bw contribution to x2 balloon plot', 'bw freq. reordered contribution to x2 balloon plot', 'bw alphab. reordered contribution to x2 balloon plot')
offa141 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'bw', 'contrib', pp_geom = "point")
offa142 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'bw', 'contrib', pp_geom = "point")
offa143 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'bw', 'contrib', pp_geom = "point")
add_float_patchwork("offa14", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
stripe <- c('color contribution to x2 balloon plot', 'color freq. reordered contribution to x2 balloon plot', 'color alphab. reordered contribution to x2 balloon plot')
offa151 <- pp_contingency(data, colnames(data[vars][1]), colnames(data[vars][2]), 'color', 'contrib', pp_geom = "point")
offa152 <- pp_contingency(data2, colnames(data2[vars][1]), colnames(data2[vars][2]), 'color', 'contrib', pp_geom = "point")
offa153 <- pp_contingency(data4, colnames(data4[vars][1]), colnames(data4[vars][2]), 'color', 'contrib', pp_geom = "point")
add_float_patchwork("offa15", 3, "w", "h", 3)
if (label == TRUE) {add_label("offa", stripe)}
rmarkdown::render(file.path(dir, "brinton_outcomes", "longplot.R"),"html_document")
pander::openFileInOS(file.path(dir, "brinton_outcomes", "longplot.html"))
}
else {print("This combination of variable types has not been considered yet")}
}
}
}
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