R/plot_topoplots_by_custom_TW.R
In aherbay/erpscope: Visualize ERPs in R
plot_topoplots_by_custom_TW <- function (data_for_map,
tw_array ,
plotname,
topoplots_scale = 'auto',
data_to_display = "voltage_difference",
levelA,
levelB,
t_test_threshold,
maps_color_palette = 'auto') {
#electrodeLocs <- readRDS("electrodeLocs_51elec.RDS")
electrodeLocs <- locations_51_electrodes
electrodeLocs <- rename(electrodeLocs, Electrode = electrode)
electrodeLocs <- subset(electrodeLocs, !(Electrode %in% c("AFz","PO5","PO6") ))
#print(head(electrodeLocs))
# base elements for topo
if (maps_color_palette == 'auto') {
jet.colors <- colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000"))
maps_color_palette <- jet.colors(10)
} else if (maps_color_palette == 'grey_gradient') {
grey.colors <- colorRampPalette(c("white", "grey"))
maps_color_palette <- grey.colors(10)
}
if(length(topoplots_scale) == 2) {
# topoplots_scale is a custom vector
} else if(topoplots_scale == 'auto') {
topoplots_scale <- c() # transforming topoplots_scale into a vector
means_by_electrodes_for_eachTime <- data_for_map %>%
group_by(Electrode,Time) %>%
summarise(Voltage= mean(Voltage) )
min_value <- abs( min(means_by_electrodes_for_eachTime$Voltage) )
max_value <- abs( max(means_by_electrodes_for_eachTime$Voltage) )
#print(min_value)
#print(max_value)
higher_value <- round(max(min_value,max_value))
topoplots_scale[1] <- -higher_value
topoplots_scale[2] <- higher_value
#print( topoplots_scale[1] )
#print( topoplots_scale[2] )
}
circleFun <- function(center = c(0,0),diameter = 1, npoints = 100) {
r = diameter / 2
tt <- seq(0,2*pi,length.out = npoints)
xx <- center[1] + r * cos(tt)
yy <- center[2] + r * sin(tt)
return(data.frame(x = xx, y = yy))
}
maskRing <- circleFun(diameter = 1.42) #create a circle round the outside of the plotting area to mask the jagged edges of the interpolation
headShape <- circleFun(c(0, 0), round(max(electrodeLocs$x)), npoints = 100) # 0
nose <- data.frame(x = c(-0.075,0,.075),y=c(.495,.575,.495))
theme_topo <- function(base_size = 12)
{
theme_bw(base_size = base_size) %+replace%
theme(
rect = element_blank(),
line = element_blank(),
axis.text = element_blank(),
axis.title = element_blank()
)
}
# for each time window
topo_ggplots <- list()
electro_ggplots <- list()
if (data_to_display %in% c("t_test_t_value", "t_test_p_value")) {
data_for_map_summarized <- data_for_map %>% group_by(Subject,Electrode,Time,Condition) %>% summarise(Voltage= mean(Voltage) )
#print(head(data_for_map_summarized))
}
# if(topoplots_scale == 'auto') {
# topoplots_scale[1] <- 0
# topoplots_scale[2] <- 0
# }
for( tw_index in 1:length(tw_array)) {
lowBound <- tw_array[[tw_index]][1]
upperBound <- tw_array[[tw_index]][2]
message(paste('--> Generating Voltage Map for Time Window: ',lowBound,"ms to",upperBound, "ms"))
if(data_to_display == "voltage_difference") {
title_legend <- "Voltage Difference"
# compute mean diff voltage for each electrode for the given time window
means_by_electrodes <- data_for_map %>%
filter ( Time > lowBound & Time < upperBound ) %>%
drop_na() %>%
group_by(Electrode)%>%
summarise(Voltage= mean(Voltage) )
# preprocess the means voltage
#print(head(means_by_electrodes))
# to solve : 1: Column `Electrode` joining factor and character vector, coercing into character vector
#electrodeLocs$Electrode <- as.factor(electrodeLocs$Electrode)
#print(unique(data$Electrode))
means_by_electrodes <- means_by_electrodes %>% right_join(electrodeLocs, by = "Electrode") %>% filter(Electrode %in% unique(data_for_map$Electrode))
#print(head(means_by_electrodes))
# if(topoplots_scale == 'auto') {
# if(topoplots_scale[1] > min(means_by_electrodes$Voltage) ) topoplots_scale[1] <- min(means_by_electrodes$Voltage)
# if(topoplots_scale[1] < max(means_by_electrodes$Voltage) ) topoplots_scale[1] <- max(means_by_electrodes$Voltage)
# }
} else if (data_to_display == "t_test_t_value") {
title_legend <- "t-test t-value"
means_by_electrodes <- data_for_map_summarized %>%
filter ( Time > lowBound & Time < upperBound ) %>%
drop_na() %>%
group_by(Subject,Electrode,Condition) %>%
summarise(
Voltage= mean(Voltage)
) %>%
group_by(Electrode) %>%
summarize(
`Voltage` = t.test( # Should change that for p value and replace voltage below by y_value_to_plot
Voltage[Condition == rlang::quo_text(levelA)],
Voltage[Condition == rlang::quo_text(levelB)], paired = TRUE
)$statistic
)
means_by_electrodes <- means_by_electrodes %>% right_join(electrodeLocs, by = "Electrode") %>% filter(Electrode %in% unique(data_for_map$Electrode))
} else if (data_to_display == "t_test_p_value") {
title_legend <- "t-test p-value"
means_by_electrodes <- data_for_map_summarized %>%
filter ( Time > lowBound & Time < upperBound ) %>%
drop_na() %>%
group_by(Subject,Electrode,Condition) %>%
summarise(
Voltage= mean(Voltage)
) %>%
group_by(Electrode)%>%
summarize(
`Voltage` = t.test( # Should change that for p value and replace voltage below by y_value_to_plot
Voltage[Condition == rlang::quo_text(levelA)],
Voltage[Condition == rlang::quo_text(levelB)], paired = TRUE
)$p.value
)
means_by_electrodes$Voltage <- means_by_electrodes$Voltage +1
means_by_electrodes <- means_by_electrodes %>% right_join(electrodeLocs, by = "Electrode") %>% filter(Electrode %in% unique(data_for_map$Electrode))
} else { stop("Invalid data_to_display in the function plot_topoplots_by_custom_TW")}
gridRes <- 250 # Specify the number of points for each grid dimension i.e. the resolution/smoothness of the interpolation
tmpTopo <- with(means_by_electrodes,
akima::interp(x = x, y = y, z = Voltage,
xo = seq(min(x)*2,
max(x)*2,
length = gridRes),
yo = seq(min(y)*2,
max(y)*2,
length = gridRes),
linear = FALSE,
extrap = TRUE)
)
interpTopo <- data.frame(x = tmpTopo$x, tmpTopo$z)
names(interpTopo)[1:length(tmpTopo$y)+1] <- tmpTopo$y
interpTopo <- gather(interpTopo,
key = y,
value = Voltage,
-x,
convert = TRUE)
interpTopo$incircle <- sqrt(interpTopo$x^2 + interpTopo$y^2) < .7 # mark grid elements that are outside of the plotting circle
interpTopo <- interpTopo[interpTopo$incircle,] #remove the elements outside the circle
# plot it
# electrodes plots
#electro_ggplots[[length(topo_ggplots) + 1]] <- ggplot(headShape,aes(x,y))+
# geom_path(size = 1.5)+
# geom_point(data = means_by_electrodes,aes(x,y,colour = Voltage),size = 3)+
# geom_line(data = nose,aes(x, y, z = NULL),size = 1.5)+
# theme_topo()+
# coord_equal()+
# labs(title = paste(lowBound,'-',upperBound))
if (data_to_display == "t_test_p_value") {
interpTopo$Voltage <- interpTopo$Voltage - 1
topo_ggplots[[length(topo_ggplots) + 1]] <- ggplot2::ggplot(interpTopo,
aes(x = x, y = y, fill = Voltage)
) +
geom_raster(show.legend=F) +
stat_contour(aes(z = Voltage),
colour = "black",
binwidth = 0.5) +
theme_topo()+
# version 1 with more gradient approach
# scale_fill_steps2(midpoint = t_test_threshold, limits = c(0,0.10), oob=scales::squish, mid = scales::muted("red"), high = "white", low = scales::muted("green", guide = FALSE) +
# version 2 with more stats threshold approach
#scale_fill_steps2(midpoint = t_test_threshold, limits = c(0,0.10), oob=scales::squish,mid = "#99cc33", high = "#339900", low = ," #ffcc00", breaks= c(0.01,0.05))+ #, breaks= c(0.01,0.05,0.05)guide = FALSE,
# version 3 essai"#297D00","#3BB300","#3390FF"
scale_fill_stepsn( limits = c(0,0.07),colors=c("#28A500","#35DA24","#00D1FF" ) , breaks= c(0.01,0.05) , values = scales::rescale(c(0.01,0.05), c(0,1)) )+
#scale_fill_stepsn( oob=scales::squish, breaks= c(0,0.001,0.01,0.05,0.05,0.10,1), colours = c("#9EBCDA", "#8C96C6", "#8C6BB1", "#88419D", "#810F7C", "#4D004B"),guide = FALSE)+ #guide = FALSE,, limits = c(0,1)
#scale_fill_stepsn(colors = c("#D73027", "#1A9850") , breaks= c(t_test_threshold) )+ # pb it changes from on VM to another
#scale_fill_steps2(midpoint = t_test_threshold, limits = c(0,0.10), breaks = c(0.001, 0.01, 0.05), mid = scales::muted("red"), high = "white", low = "red" , guide = FALSE)+ #, breaks= c(0,0.001,0.01,0.05,0.05,0.10,1)
geom_path(data = maskRing,
aes(x, y, z = NULL, fill =NULL),
colour = "white",
size = 15)+
geom_point(data = means_by_electrodes,
aes(x, y),
size = 1)+
geom_path(data = headShape,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
geom_path(data = nose,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
coord_equal()+theme(plot.title = element_text(hjust = 0.5,vjust = -4))+
labs(title = paste(lowBound,'ms to',upperBound, 'ms'))
}else {
topo_ggplots[[length(topo_ggplots) + 1]] <- ggplot2::ggplot(interpTopo,
aes(x = x, y = y, fill = Voltage)
) +
geom_raster(show.legend=F) +
stat_contour(aes(z = Voltage),
colour = "black",
binwidth = 0.5) +
theme_topo()+
scale_fill_gradientn(colours = maps_color_palette,
limits = c(topoplots_scale[1],topoplots_scale[2]),
guide = FALSE, #"colourbar"
oob = scales::squish) +
geom_path(data = maskRing,
aes(x, y, z = NULL, fill =NULL),
colour = "white",
size = 15)+
geom_point(data = means_by_electrodes,
aes(x, y),
size = 1)+
geom_path(data = headShape,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
geom_path(data = nose,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
coord_equal()+theme(plot.title = element_text(hjust = 0.5,vjust = -4))+
labs(title = paste(lowBound,'ms to',upperBound, 'ms'))
}
# last plot to get legend
if(tw_index == length(tw_array) ){
if(data_to_display == "t_test_p_value" ) {
#print(t_test_threshold)
topo_forlegend <- ggplot2::ggplot(interpTopo,
aes(x = x, y = y, fill = Voltage)
) +
geom_raster(show.legend=F) +
stat_contour(aes(z = Voltage),
colour = "black",
binwidth = 0.5) +
theme_topo()+
theme(legend.position="bottom",
legend.background = element_rect(fill = "transparent", colour = "transparent"))+
#scale_fill_steps2(midpoint = t_test_threshold, limits = c(0,0.10), mid = scales::muted("red"), high = "white", low = "red")+ #, breaks= c(0,0.001,0.01,0.05,0.05,0.10,1)
#scale_fill_stepsn( breaks= c(0,0.001,0.01,0.05,0.05,0.10,1), colours = c("#9EBCDA", "#8C96C6", "#8C6BB1", "#88419D", "#810F7C", "#4D004B"),guide = FALSE)+ #guide = FALSE,, limits = c(0,1)
#scale_fill_steps2(midpoint = t_test_threshold, limits = c(0,0.10),oob=scales::squish, mid = scales::muted("red"), high = "white", low = scales::muted("green") , guide = FALSE)+ #, breaks= c(0,0.001,0.01,0.05,0.05,0.10,1)
scale_fill_stepsn( limits = c(0,0.07), oob=scales::squish,colors=c("#28A500","#35DA24","#00D1FF") , breaks= c(0.01,0.05) , values = scales::rescale(c(0.01,0.05), c(0,1)),
guide = guide_coloursteps(even.steps = TRUE,show.limits = TRUE ) )+ # ffcc00 c("#339900","#99cc33","#3390FF") FFE033 FAE7D2 purple-blue 28A500
#scale_fill_stepsn(colors = c("#FC8D59", "#FEE08B","#D9EF8B", "#91CF60", "#1A9850") ,
# breaks = c(0.001, 0.01, 0.05, 0.10))+
guides(fill = guide_colourbar(barwidth = 10))+
geom_path(data = maskRing,
aes(x, y, z = NULL, fill =NULL),
colour = "white",
size = 15)+
geom_point(data = means_by_electrodes,
aes(x, y),
size = 1)+
geom_path(data = headShape,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
geom_path(data = nose,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
coord_equal()+theme(plot.title = element_text(hjust = 0.5,vjust = -4))+
labs(title = paste(lowBound,'ms to',upperBound, 'ms'), fill = paste(title_legend," "))
} else {
#highest_abs_viltage <- max(abs(topoplots_scale[1]),abs(topoplots_scale[2]))
#topoplots_scale[1] <-
topo_forlegend <- ggplot2::ggplot(interpTopo,
aes(x = x, y = y, fill = Voltage)
) +
geom_raster(show.legend=F) +
stat_contour(aes(z = Voltage),
colour = "black",
binwidth = 0.5) +
theme_topo()+
theme(legend.position="bottom",
legend.background = element_rect(fill = "transparent", colour = "transparent"))+
scale_fill_gradientn(colours = maps_color_palette,
limits = c(topoplots_scale[1],topoplots_scale[2]),
oob = scales::squish,
breaks= seq(round(topoplots_scale[1]),round(topoplots_scale[2]), round(topoplots_scale[2]/3) ),
labels= seq(round(topoplots_scale[1]),round(topoplots_scale[2]), round(topoplots_scale[2]/3) ) ) +
guides(fill = guide_colourbar(barwidth = 10))+
geom_path(data = maskRing,
aes(x, y, z = NULL, fill =NULL),
colour = "white",
size = 15)+
geom_point(data = means_by_electrodes,
aes(x, y),
size = 1)+
geom_path(data = headShape,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
geom_path(data = nose,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
coord_equal()+theme(plot.title = element_text(hjust = 0.5,vjust = -2))+
labs(title = paste(lowBound,'ms to',upperBound, 'ms'), fill = paste(title_legend," "))
}
# legend <- ggpubr::get_legend( topo_forlegend )
legend <- ggpubr::get_legend( topo_forlegend )
#topolegend <- cowplot::plot_grid(NULL, legend, ncol=1)
topolegend <- ggpubr::as_ggplot(legend)
#saveRDS(topolegend, "legend.RDS")
}
}
topo_ggplots_with_legend <- list(topo_ggplots,topolegend)
#ggarrange(plotlist=topo_ggplots, nrow = 1, ncol = 6)
# ggsave(filename=paste(plotname, "topo",'_',min_time,'-',max_time,'.pdf', sep=''), width = 20, height = 8)
#ggarrange(plotlist=electro_ggplots, nrow = 4, ncol = 10)
#ggsave(filename=paste("electro",'_',min_time,'-',max_time,'.pdf', sep=''))
return(topo_ggplots_with_legend)
}
aherbay/erpscope documentation built on Feb. 1, 2024, 7:56 p.m.
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plot_topoplots_by_custom_TW <- function (data_for_map,
tw_array ,
plotname,
topoplots_scale = 'auto',
data_to_display = "voltage_difference",
levelA,
levelB,
t_test_threshold,
maps_color_palette = 'auto') {
#electrodeLocs <- readRDS("electrodeLocs_51elec.RDS")
electrodeLocs <- locations_51_electrodes
electrodeLocs <- rename(electrodeLocs, Electrode = electrode)
electrodeLocs <- subset(electrodeLocs, !(Electrode %in% c("AFz","PO5","PO6") ))
#print(head(electrodeLocs))
# base elements for topo
if (maps_color_palette == 'auto') {
jet.colors <- colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000"))
maps_color_palette <- jet.colors(10)
} else if (maps_color_palette == 'grey_gradient') {
grey.colors <- colorRampPalette(c("white", "grey"))
maps_color_palette <- grey.colors(10)
}
if(length(topoplots_scale) == 2) {
# topoplots_scale is a custom vector
} else if(topoplots_scale == 'auto') {
topoplots_scale <- c() # transforming topoplots_scale into a vector
means_by_electrodes_for_eachTime <- data_for_map %>%
group_by(Electrode,Time) %>%
summarise(Voltage= mean(Voltage) )
min_value <- abs( min(means_by_electrodes_for_eachTime$Voltage) )
max_value <- abs( max(means_by_electrodes_for_eachTime$Voltage) )
#print(min_value)
#print(max_value)
higher_value <- round(max(min_value,max_value))
topoplots_scale[1] <- -higher_value
topoplots_scale[2] <- higher_value
#print( topoplots_scale[1] )
#print( topoplots_scale[2] )
}
circleFun <- function(center = c(0,0),diameter = 1, npoints = 100) {
r = diameter / 2
tt <- seq(0,2*pi,length.out = npoints)
xx <- center[1] + r * cos(tt)
yy <- center[2] + r * sin(tt)
return(data.frame(x = xx, y = yy))
}
maskRing <- circleFun(diameter = 1.42) #create a circle round the outside of the plotting area to mask the jagged edges of the interpolation
headShape <- circleFun(c(0, 0), round(max(electrodeLocs$x)), npoints = 100) # 0
nose <- data.frame(x = c(-0.075,0,.075),y=c(.495,.575,.495))
theme_topo <- function(base_size = 12)
{
theme_bw(base_size = base_size) %+replace%
theme(
rect = element_blank(),
line = element_blank(),
axis.text = element_blank(),
axis.title = element_blank()
)
}
# for each time window
topo_ggplots <- list()
electro_ggplots <- list()
if (data_to_display %in% c("t_test_t_value", "t_test_p_value")) {
data_for_map_summarized <- data_for_map %>% group_by(Subject,Electrode,Time,Condition) %>% summarise(Voltage= mean(Voltage) )
#print(head(data_for_map_summarized))
}
# if(topoplots_scale == 'auto') {
# topoplots_scale[1] <- 0
# topoplots_scale[2] <- 0
# }
for( tw_index in 1:length(tw_array)) {
lowBound <- tw_array[[tw_index]][1]
upperBound <- tw_array[[tw_index]][2]
message(paste('--> Generating Voltage Map for Time Window: ',lowBound,"ms to",upperBound, "ms"))
if(data_to_display == "voltage_difference") {
title_legend <- "Voltage Difference"
# compute mean diff voltage for each electrode for the given time window
means_by_electrodes <- data_for_map %>%
filter ( Time > lowBound & Time < upperBound ) %>%
drop_na() %>%
group_by(Electrode)%>%
summarise(Voltage= mean(Voltage) )
# preprocess the means voltage
#print(head(means_by_electrodes))
# to solve : 1: Column `Electrode` joining factor and character vector, coercing into character vector
#electrodeLocs$Electrode <- as.factor(electrodeLocs$Electrode)
#print(unique(data$Electrode))
means_by_electrodes <- means_by_electrodes %>% right_join(electrodeLocs, by = "Electrode") %>% filter(Electrode %in% unique(data_for_map$Electrode))
#print(head(means_by_electrodes))
# if(topoplots_scale == 'auto') {
# if(topoplots_scale[1] > min(means_by_electrodes$Voltage) ) topoplots_scale[1] <- min(means_by_electrodes$Voltage)
# if(topoplots_scale[1] < max(means_by_electrodes$Voltage) ) topoplots_scale[1] <- max(means_by_electrodes$Voltage)
# }
} else if (data_to_display == "t_test_t_value") {
title_legend <- "t-test t-value"
means_by_electrodes <- data_for_map_summarized %>%
filter ( Time > lowBound & Time < upperBound ) %>%
drop_na() %>%
group_by(Subject,Electrode,Condition) %>%
summarise(
Voltage= mean(Voltage)
) %>%
group_by(Electrode) %>%
summarize(
`Voltage` = t.test( # Should change that for p value and replace voltage below by y_value_to_plot
Voltage[Condition == rlang::quo_text(levelA)],
Voltage[Condition == rlang::quo_text(levelB)], paired = TRUE
)$statistic
)
means_by_electrodes <- means_by_electrodes %>% right_join(electrodeLocs, by = "Electrode") %>% filter(Electrode %in% unique(data_for_map$Electrode))
} else if (data_to_display == "t_test_p_value") {
title_legend <- "t-test p-value"
means_by_electrodes <- data_for_map_summarized %>%
filter ( Time > lowBound & Time < upperBound ) %>%
drop_na() %>%
group_by(Subject,Electrode,Condition) %>%
summarise(
Voltage= mean(Voltage)
) %>%
group_by(Electrode)%>%
summarize(
`Voltage` = t.test( # Should change that for p value and replace voltage below by y_value_to_plot
Voltage[Condition == rlang::quo_text(levelA)],
Voltage[Condition == rlang::quo_text(levelB)], paired = TRUE
)$p.value
)
means_by_electrodes$Voltage <- means_by_electrodes$Voltage +1
means_by_electrodes <- means_by_electrodes %>% right_join(electrodeLocs, by = "Electrode") %>% filter(Electrode %in% unique(data_for_map$Electrode))
} else { stop("Invalid data_to_display in the function plot_topoplots_by_custom_TW")}
gridRes <- 250 # Specify the number of points for each grid dimension i.e. the resolution/smoothness of the interpolation
tmpTopo <- with(means_by_electrodes,
akima::interp(x = x, y = y, z = Voltage,
xo = seq(min(x)*2,
max(x)*2,
length = gridRes),
yo = seq(min(y)*2,
max(y)*2,
length = gridRes),
linear = FALSE,
extrap = TRUE)
)
interpTopo <- data.frame(x = tmpTopo$x, tmpTopo$z)
names(interpTopo)[1:length(tmpTopo$y)+1] <- tmpTopo$y
interpTopo <- gather(interpTopo,
key = y,
value = Voltage,
-x,
convert = TRUE)
interpTopo$incircle <- sqrt(interpTopo$x^2 + interpTopo$y^2) < .7 # mark grid elements that are outside of the plotting circle
interpTopo <- interpTopo[interpTopo$incircle,] #remove the elements outside the circle
# plot it
# electrodes plots
#electro_ggplots[[length(topo_ggplots) + 1]] <- ggplot(headShape,aes(x,y))+
# geom_path(size = 1.5)+
# geom_point(data = means_by_electrodes,aes(x,y,colour = Voltage),size = 3)+
# geom_line(data = nose,aes(x, y, z = NULL),size = 1.5)+
# theme_topo()+
# coord_equal()+
# labs(title = paste(lowBound,'-',upperBound))
if (data_to_display == "t_test_p_value") {
interpTopo$Voltage <- interpTopo$Voltage - 1
topo_ggplots[[length(topo_ggplots) + 1]] <- ggplot2::ggplot(interpTopo,
aes(x = x, y = y, fill = Voltage)
) +
geom_raster(show.legend=F) +
stat_contour(aes(z = Voltage),
colour = "black",
binwidth = 0.5) +
theme_topo()+
# version 1 with more gradient approach
# scale_fill_steps2(midpoint = t_test_threshold, limits = c(0,0.10), oob=scales::squish, mid = scales::muted("red"), high = "white", low = scales::muted("green", guide = FALSE) +
# version 2 with more stats threshold approach
#scale_fill_steps2(midpoint = t_test_threshold, limits = c(0,0.10), oob=scales::squish,mid = "#99cc33", high = "#339900", low = ," #ffcc00", breaks= c(0.01,0.05))+ #, breaks= c(0.01,0.05,0.05)guide = FALSE,
# version 3 essai"#297D00","#3BB300","#3390FF"
scale_fill_stepsn( limits = c(0,0.07),colors=c("#28A500","#35DA24","#00D1FF" ) , breaks= c(0.01,0.05) , values = scales::rescale(c(0.01,0.05), c(0,1)) )+
#scale_fill_stepsn( oob=scales::squish, breaks= c(0,0.001,0.01,0.05,0.05,0.10,1), colours = c("#9EBCDA", "#8C96C6", "#8C6BB1", "#88419D", "#810F7C", "#4D004B"),guide = FALSE)+ #guide = FALSE,, limits = c(0,1)
#scale_fill_stepsn(colors = c("#D73027", "#1A9850") , breaks= c(t_test_threshold) )+ # pb it changes from on VM to another
#scale_fill_steps2(midpoint = t_test_threshold, limits = c(0,0.10), breaks = c(0.001, 0.01, 0.05), mid = scales::muted("red"), high = "white", low = "red" , guide = FALSE)+ #, breaks= c(0,0.001,0.01,0.05,0.05,0.10,1)
geom_path(data = maskRing,
aes(x, y, z = NULL, fill =NULL),
colour = "white",
size = 15)+
geom_point(data = means_by_electrodes,
aes(x, y),
size = 1)+
geom_path(data = headShape,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
geom_path(data = nose,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
coord_equal()+theme(plot.title = element_text(hjust = 0.5,vjust = -4))+
labs(title = paste(lowBound,'ms to',upperBound, 'ms'))
}else {
topo_ggplots[[length(topo_ggplots) + 1]] <- ggplot2::ggplot(interpTopo,
aes(x = x, y = y, fill = Voltage)
) +
geom_raster(show.legend=F) +
stat_contour(aes(z = Voltage),
colour = "black",
binwidth = 0.5) +
theme_topo()+
scale_fill_gradientn(colours = maps_color_palette,
limits = c(topoplots_scale[1],topoplots_scale[2]),
guide = FALSE, #"colourbar"
oob = scales::squish) +
geom_path(data = maskRing,
aes(x, y, z = NULL, fill =NULL),
colour = "white",
size = 15)+
geom_point(data = means_by_electrodes,
aes(x, y),
size = 1)+
geom_path(data = headShape,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
geom_path(data = nose,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
coord_equal()+theme(plot.title = element_text(hjust = 0.5,vjust = -4))+
labs(title = paste(lowBound,'ms to',upperBound, 'ms'))
}
# last plot to get legend
if(tw_index == length(tw_array) ){
if(data_to_display == "t_test_p_value" ) {
#print(t_test_threshold)
topo_forlegend <- ggplot2::ggplot(interpTopo,
aes(x = x, y = y, fill = Voltage)
) +
geom_raster(show.legend=F) +
stat_contour(aes(z = Voltage),
colour = "black",
binwidth = 0.5) +
theme_topo()+
theme(legend.position="bottom",
legend.background = element_rect(fill = "transparent", colour = "transparent"))+
#scale_fill_steps2(midpoint = t_test_threshold, limits = c(0,0.10), mid = scales::muted("red"), high = "white", low = "red")+ #, breaks= c(0,0.001,0.01,0.05,0.05,0.10,1)
#scale_fill_stepsn( breaks= c(0,0.001,0.01,0.05,0.05,0.10,1), colours = c("#9EBCDA", "#8C96C6", "#8C6BB1", "#88419D", "#810F7C", "#4D004B"),guide = FALSE)+ #guide = FALSE,, limits = c(0,1)
#scale_fill_steps2(midpoint = t_test_threshold, limits = c(0,0.10),oob=scales::squish, mid = scales::muted("red"), high = "white", low = scales::muted("green") , guide = FALSE)+ #, breaks= c(0,0.001,0.01,0.05,0.05,0.10,1)
scale_fill_stepsn( limits = c(0,0.07), oob=scales::squish,colors=c("#28A500","#35DA24","#00D1FF") , breaks= c(0.01,0.05) , values = scales::rescale(c(0.01,0.05), c(0,1)),
guide = guide_coloursteps(even.steps = TRUE,show.limits = TRUE ) )+ # ffcc00 c("#339900","#99cc33","#3390FF") FFE033 FAE7D2 purple-blue 28A500
#scale_fill_stepsn(colors = c("#FC8D59", "#FEE08B","#D9EF8B", "#91CF60", "#1A9850") ,
# breaks = c(0.001, 0.01, 0.05, 0.10))+
guides(fill = guide_colourbar(barwidth = 10))+
geom_path(data = maskRing,
aes(x, y, z = NULL, fill =NULL),
colour = "white",
size = 15)+
geom_point(data = means_by_electrodes,
aes(x, y),
size = 1)+
geom_path(data = headShape,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
geom_path(data = nose,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
coord_equal()+theme(plot.title = element_text(hjust = 0.5,vjust = -4))+
labs(title = paste(lowBound,'ms to',upperBound, 'ms'), fill = paste(title_legend," "))
} else {
#highest_abs_viltage <- max(abs(topoplots_scale[1]),abs(topoplots_scale[2]))
#topoplots_scale[1] <-
topo_forlegend <- ggplot2::ggplot(interpTopo,
aes(x = x, y = y, fill = Voltage)
) +
geom_raster(show.legend=F) +
stat_contour(aes(z = Voltage),
colour = "black",
binwidth = 0.5) +
theme_topo()+
theme(legend.position="bottom",
legend.background = element_rect(fill = "transparent", colour = "transparent"))+
scale_fill_gradientn(colours = maps_color_palette,
limits = c(topoplots_scale[1],topoplots_scale[2]),
oob = scales::squish,
breaks= seq(round(topoplots_scale[1]),round(topoplots_scale[2]), round(topoplots_scale[2]/3) ),
labels= seq(round(topoplots_scale[1]),round(topoplots_scale[2]), round(topoplots_scale[2]/3) ) ) +
guides(fill = guide_colourbar(barwidth = 10))+
geom_path(data = maskRing,
aes(x, y, z = NULL, fill =NULL),
colour = "white",
size = 15)+
geom_point(data = means_by_electrodes,
aes(x, y),
size = 1)+
geom_path(data = headShape,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
geom_path(data = nose,
aes(x, y, z = NULL, fill = NULL),
size = 1.5)+
coord_equal()+theme(plot.title = element_text(hjust = 0.5,vjust = -2))+
labs(title = paste(lowBound,'ms to',upperBound, 'ms'), fill = paste(title_legend," "))
}
# legend <- ggpubr::get_legend( topo_forlegend )
legend <- ggpubr::get_legend( topo_forlegend )
#topolegend <- cowplot::plot_grid(NULL, legend, ncol=1)
topolegend <- ggpubr::as_ggplot(legend)
#saveRDS(topolegend, "legend.RDS")
}
}
topo_ggplots_with_legend <- list(topo_ggplots,topolegend)
#ggarrange(plotlist=topo_ggplots, nrow = 1, ncol = 6)
# ggsave(filename=paste(plotname, "topo",'_',min_time,'-',max_time,'.pdf', sep=''), width = 20, height = 8)
#ggarrange(plotlist=electro_ggplots, nrow = 4, ncol = 10)
#ggsave(filename=paste("electro",'_',min_time,'-',max_time,'.pdf', sep=''))
return(topo_ggplots_with_legend)
}
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