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new implementation of timecourse plots testing
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@craddm
craddm committed Jul 29, 2018
1 parent 7134e76 commit 30ecbeb
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Showing 2 changed files with 307 additions and 78 deletions.
128 changes: 90 additions & 38 deletions R/erp_scalp.R
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
#' @details The function uses default electrode names and locations contained
#' in the package.
#'
#' @author Matti Vuorre, \email{[email protected]}
#' @author Matti Vuorre, \email{mv2521@@columbia.edu}
#' @importFrom purrr map
#' @import dplyr
#' @import ggplot2
Expand All @@ -39,15 +39,23 @@ erp_scalp <- function(data,
montage = NULL) {

if (is.eeg_epochs(data)) {
data <- as.data.frame(data, long = TRUE)
data <- as.data.frame(data,
long = TRUE)
}

if (is.null(color)) {
data <- dplyr::group_by(data, electrode, time)
data <- dplyr::summarise(data, amplitude = mean(amplitude))
data <- dplyr::group_by(data,
electrode,
time)
data <- dplyr::summarise(data,
amplitude = mean(amplitude))
} else {
data <- dplyr::group_by_(data, electrode, time, as.name(color))
data <- dplyr::summarise(data, amplitude = mean(amplitude))
data <- dplyr::group_by_(data,
electrode,
time,
as.name(color))
data <- dplyr::summarise(data,
amplitude = mean(amplitude))
}

data <- as.data.frame(data)
Expand Down Expand Up @@ -96,37 +104,54 @@ erp_scalp <- function(data,
data <- dplyr::select(data, -data)

# Get default electrode locations from pkg internal data
data <- electrode_locations(data, drop = T, montage = montage)
data <- electrode_locations(data,
drop = T,
montage = montage)

p <- ggplot(data, aes(x, y)) +
p <- ggplot(data,
aes(x, y)) +
geom_blank() +
theme_void() +
theme(plot.margin = unit(c(8, 8, 8, 8), "pt"))

guide <- ggplot(data, aes(x = time, y = amplitude)) +
coord_cartesian(ylim = c(minAmp, maxAmp),
xlim = c(minTime, maxTime)) +
guide <- ggplot(data,
aes(x = time,
y = amplitude)) +
coord_cartesian(ylim = c(minAmp,
maxAmp),
xlim = c(minTime,
maxTime)) +
scale_x_continuous(breaks = scales::pretty_breaks(n = 3)) +
scale_y_continuous(breaks = scales::pretty_breaks(n = 3)) +
geom_vline(xintercept = 0, size = .4) +
geom_hline(yintercept = 0, size = .4) +
labs(y = expression(paste("Amplitude (", mu, "V)")),
geom_vline(xintercept = 0,
size = .4) +
geom_hline(yintercept = 0,
size = .4) +
labs(y = expression(paste("Amplitude (",
mu,
"V)")),
x = "Time (s)") +
theme_minimal(base_size = 8) +
theme(panel.grid = element_blank(),
axis.ticks = element_line(size = .3),
plot.margin = unit(c(8, 8, 8, 8), "pt"))

if (show_guide) {
p <- p +
annotation_custom(grob = ggplotGrob(guide),
xmin = min(data$x) - .07, xmax = min(data$x) + .09,
ymin = min(data$y) - .09, ymax = min(data$y) + .09)
xmin = min(data$x) - .07,
xmax = min(data$x) + .09,
ymin = min(data$y) - .09,
ymax = min(data$y) + .09)
}

for (i in 1:nrow(data)) {
p <- p +
annotation_custom(grob = ggplotGrob(data$plot[[i]]),
xmin = data$x[i] - .05, xmax = data$x[i] + .05,
ymin = data$y[i] - .07, ymax = data$y[i] + .07)
xmin = data$x[i] - .05,
xmax = data$x[i] + .05,
ymin = data$y[i] - .07,
ymax = data$y[i] + .07)
}

return(p)
Expand All @@ -142,26 +167,28 @@ erp_scalp <- function(data,
#' @param data An EEG dataset.
#' @param colour Variable to colour lines by. If no variable is passed, only one
#' line is drawn for each electrode.
#' @param baseline Character vector of times to subtract for baseline correct.
#' @param baseline Character vector of times to subtract for baseline correction.
#' @param montage Name of an existing montage set. Defaults to NULL; (currently
#' only 'biosemi64alpha' available other than default 10/20 system)
#'
#' @author Matt Craddock, \email{[email protected]}
#' @author Matt Craddock, \email{matt@@mattcraddock.com}
#'
#' @import shiny
#' @import miniUI
#' @export

interactive_scalp <- function(data, colour = NULL,
baseline = NULL, montage = NULL) {
interactive_scalp <- function(data,
colour = NULL,
baseline = NULL,
montage = NULL) {

if (is.eeg_data(data)) {
data <- eeg_average(data)
data <- as.data.frame(data, long = TRUE)
}

if (!is.null(baseline)) {
data <- rm_baseline(data, time_lim = baseline)
data <- rm_baseline(data,
time_lim = baseline)
}

ui <- miniPage(
Expand Down Expand Up @@ -192,24 +219,38 @@ interactive_scalp <- function(data, colour = NULL,
)
)

server <- function(input, output, session) {
server <- function(input,
output,
session) {

data <- electrode_locations(data, drop = TRUE, montage = montage)
tmp_data <- as.data.frame(data,
long = TRUE)
tmp_data <- electrode_locations(tmp_data,
drop = TRUE,
montage = montage)

button_reacts <- reactiveValues(sel_elecs = list(), avg = TRUE)
button_reacts <- reactiveValues(sel_elecs = list(),
avg = TRUE)

output$Scalp <- renderPlot({

if (is.null(colour)) {
erp_scalp(data, montage = montage)
erp_scalp(tmp_data,
montage = montage)
} else {
erp_scalp(data, color = as.name(colour), montage = montage)
erp_scalp(tmp_data,
color = as.name(colour),
montage = montage)
}

})

observeEvent(input$click_plot, {

tmp <- nearPoints(data, input$click_plot,
"x", "y", threshold = 45,
tmp <- nearPoints(tmp_data,
input$click_plot,
"x", "y",
threshold = 45,
maxpoints = 1)

if (nrow(tmp) > 0) {
Expand All @@ -229,18 +270,29 @@ interactive_scalp <- function(data, colour = NULL,
output$Selected <- renderPlot({
if (button_reacts$avg) {
if (is.null(colour)) {
plot_timecourse(data[data$electrode %in% button_reacts$sel_elecs, ])
#plot_timecourse(data[data$electrode %in% button_reacts$sel_elecs, ])
plot_tc(select_elecs(data,
button_reacts$sel_elecs))
} else {
plot_timecourse(data[data$electrode %in% button_reacts$sel_elecs, ],
colour = as.name(colour))
plot_tc(select_elecs(data,
button_reacts$sel_elecs),
colour = as.name(colour))
#plot_timecourse(data[data$electrode %in% button_reacts$sel_elecs, ],
# colour = as.name(colour))
}
} else {
if (is.null(colour)) {
plot_timecourse(data[data$electrode %in% button_reacts$sel_elecs, ],
colour = "electrode")
plot_tc(select_elecs(data,
button_reacts$sel_elecs),
colour = "electrode")
#plot_timecourse(data[data$electrode %in% button_reacts$sel_elecs, ],
# colour = "electrode")
} else{
plot_timecourse(data[data$electrode %in% button_reacts$sel_elecs, ],
colour = as.name(colour)) +
plot_tc(select_elecs(data,
button_reacts$sel_elecs),
colour = as.name(colour)) +
# plot_timecourse(data[data$electrode %in% button_reacts$sel_elecs, ],
# colour = as.name(colour)) +
facet_wrap(~electrode)
}
}
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