Added supports for phantom channels

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ravedash
 Type: Package
 Title: Dashboard System for Reproducible Visualization of 'iEEG'
-Version: 0.1.3.21
+Version: 0.1.3.22
 Authors@R: c(
     person("Zhengjia", "Wang", email = "dipterix.wang@gmail.com", role = c("aut", "cre", "cph"))
     )
@@ -15,6 +15,8 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 Language: en-US
 Imports: 
+    grDevices,
+    stats,
     dipsaus (>= 0.2.0),
     logger (>= 0.2.2),
     raveio (>= 0.0.6),

NAMESPACE

@@ -20,7 +20,6 @@ S3method(remove_session,default)
 S3method(use_session,"rave-dash-session")
 S3method(use_session,default)
 export("%OF%")
-export(RAVEPlotContainer)
 export(be_patient_text)
 export(card_badge)
 export(card_href)

R/aaa.R

@@ -10,6 +10,139 @@ gray_label_color <- "#c8c9ca"
 
 ansi_regex <- "(?:(?:\\x{001b}\\[)|\\x{009b})(?:(?:[0-9]{1,3})?(?:(?:;[0-9]{0,3})*)?[A-M|f-m])|\\x{001b}[A-M]"
 
+
+DEFAULT_PALETTES <- local({
+
+  LINE <- list(
+    'Beautiful Field' = c("orange", "dodgerblue3", "darkgreen", "orangered", "brown",  "purple3"),
+    'J5' = c("#407899","#deba6f", "#65743a", "#de6449", "#4B296B"),
+    'Okabe-Ito' = c("black", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2",
+                    "#D55E00", "#CC79A7", "gray60"),
+    'Okabe-Ito 2' = c("#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2",
+                      "#D55E00", "#CC79A7", "gray60"),
+    'Black+tan' = c('#1A1A19', '#A25D34', '#353634', '#D0A380'),
+    'Accent' = c('#7fc97f','#beaed4','#fdc086','#ffff99','#386cb0','#f0027f','#bf5b17','#656565'),
+    'Dark2' = c('#1b9e77','#d95f02','#7570b3','#e7298a','#66a61e','#e6ab02','#a6761d','#656565'),
+    'R4' = c("black", "#DF536B", "#61D04F", "#2297E6", "#28E2E5", "#CD0BBC", "#F5C710", "gray62"),
+    'R4Permed' = c("#2297E6", "#F5C710", "#61D04F", "#DF536B", "#CD0BBC"),
+    'Paired' = c('#a6cee3','#1f78b4','#b2df8a','#33a02c','#fb9a99','#e31a1c','#fdbf6f','#ff7f00'),
+    'Pastel1' = c('#fbb4ae','#b3cde3','#ccebc5','#decbe4','#fed9a6','#ffffcc','#e5d8bd','#fddaec'),
+    'Pastel2' = c('#b3e2cd','#fdcdac','#cbd5e8','#f4cae4','#e6f5c9','#fff2ae','#f1e2cc','#cccccc'),
+    'Set1' = c('#e41a1c','#377eb8','#4daf4a','#984ea3','#ff7f00','#ffff33','#a65628','#f781bf'),
+    'Set2' = c('#66c2a5','#fc8d62','#8da0cb','#e78ac3','#a6d854','#ffd92f','#e5c494','#b3b3b3'),
+    'Set3' = c('#8dd3c7','#ffffb3','#bebada','#fb8072','#80b1d3','#fdb462','#b3de69','#fccde5')
+  )
+
+  HEATMAP <- list(
+    BlueWhiteRed = rev(c("#67001f", "#b2182b", "#d6604d", "#f4a582", "#fddbc7", "#ffffff",
+                         "#d1e5f0", "#92c5de", "#4393c3", "#2166ac", "#053061")),
+    BlueGrayRed = rev(c("#67001f", "#b2182b", "#d6604d", "#f4a582", "#b4b4b4",
+                        "#92c5de", "#4393c3", "#2166ac", "#053061")),
+    Spectral = rev(c('#9e0142','#d53e4f','#f46d43','#fdae61','#fee08b','#ffffbf',
+                     '#e6f598','#abdda4','#66c2a5','#3288bd','#5e4fa2')),
+    BrownWhiteGreen = c('#543005','#8c510a','#bf812d','#dfc27d','#f6e8c3','#f5f5f5',
+                        '#c7eae5','#80cdc1','#35978f','#01665e','#003c30'),
+    PinkWhiteGreen =c('#8e0152','#c51b7d','#de77ae','#f1b6da','#fde0ef','#f7f7f7',
+                      '#e6f5d0','#b8e186','#7fbc41','#4d9221','#276419'),
+    PurpleWhiteGreen = c('#40004b','#762a83','#9970ab','#c2a5cf','#e7d4e8','#f7f7f7',
+                         '#d9f0d3','#a6dba0','#5aae61','#1b7837','#00441b'),
+    OrangeWhitePurple = c('#7f3b08','#b35806','#e08214','#fdb863','#fee0b6','#f7f7f7',
+                          '#d8daeb','#b2abd2','#8073ac','#542788','#2d004b'),
+    BlackWhiteRed = rev(c('#67001f','#b2182b','#d6604d','#f4a582','#fddbc7','#ffffff',
+                          '#e0e0e0','#bababa','#878787','#4d4d4d','#1a1a1a')),
+    BlueYellowRed = rev(c('#a50026','#d73027','#f46d43','#fdae61','#fee090','#ffffbf',
+                          '#e0f3f8','#abd9e9','#74add1','#4575b4','#313695')),
+    GreenYellowRed = rev(c('#a50026','#d73027','#f46d43','#fdae61','#fee08b','#ffffbf',
+                           '#d9ef8b','#a6d96a','#66bd63','#1a9850','#006837'))
+  )
+
+
+  set <- function(type = c("line", "heatmap"), name, col) {
+    stopifnot2(length(col) >= 3, msg = "length(col) must >= 3 to set a palette")
+    type <- match.arg(type)
+    if(type == "line") {
+      LINE[[ name ]] <<- col
+    } else {
+      HEATMAP[[ name ]] <<- col
+    }
+    invisible(name)
+  }
+
+  get <- function(name, type = c("line", "heatmap"), get_palettes = FALSE, get_palette_names = FALSE) {
+    type <- match.arg(type)
+
+    if(type == "line") {
+      pals <- LINE
+    } else {
+      pals <- HEATMAP
+    }
+
+    if(missing(name)) {
+      if( get_palette_names ) {
+        return (names(pals))
+      }
+      return (pals)
+    }
+
+    if(!length(name)) {
+      logger("Invalid palette requested: [{deparse1(name)}]. Returning the first palette", level = "warning", use_glue = TRUE)
+      pal <- pals[[1]]
+    } else {
+      pal <- pals[[ name ]]
+    }
+
+    attr(pal, "name") <- name
+    return (pal)
+  }
+
+  return(list(
+    set = set,
+    get = get
+  ))
+
+})
+
+DEFAULT_GRAPHICS <- list(
+  rave_cex.main = 1.5,
+  rave_cex.axis = 1.3,
+  # putting this to 1.4 because 1.5 causes some clipping of the axis(2) label, we could also try to increase
+  # the (outer) left margin to compensate
+  rave_cex.lab = 1.4,
+  rave_axis_tcl = -0.3,
+  plot_time_range = c(-Inf,Inf),
+  draw_decorator_labels = FALSE,
+  plot_title_options = c('Subject ID', 'Electrode #', 'Condition', 'Frequency Range',
+                         'Sample Size', 'Baseline Window', 'Analysis Window'),
+
+  # no shiny, shiny running, all(mfrow == 2), any(mfrow > 2)
+  cex_multiplier = c(1, 1/0.88, 1/0.66),
+
+  ## this is now managed through ravedash theme
+  background_plot_color_hint = 'white',
+  champions_tunic = '#009edd',
+
+  invert_colors_in_palette = FALSE,
+  reverse_colors_in_palette = FALSE,
+
+  analysis_window.shade.color = 'gray70',
+  analysis_window.stroke.color = 'match',
+
+  heatmap_number_color_values = 101,
+  invert_colors_in_heatmap_palette = FALSE,
+  reverse_colors_in_heatmap_palette = FALSE,
+
+  show_outliers_on_plots = TRUE,
+
+  log_scale = FALSE,
+  max_zlim = 0,
+  percentile_range = TRUE,
+  sort_trials_by_type = 'Trial Number',
+
+  max_columns_in_figure = 3
+)
+
+
+
 strip_style <- function(x, ...) {
   gsub(ansi_regex, "", x, perl = TRUE, useBytes = TRUE)
 }