Merge pull request #3 from beauchamplab/dev

Dev

DESCRIPTION

@@ -1,37 +1,50 @@
 # Generated by roxygen2: do not edit by hand
 Package: ravebuiltins
 Type: Package
-Title: What the Package Does (Title Case)
-Version: 0.1.0
-Description: More about what it does (maybe more than one line)
-    Use four spaces when indenting paragraphs within the Description.
+Title: Builtin Modules for `RAVE`
+Version: 0.1.1
+Description: This package provides builtin modules for `RAVE`. It aims at analyze 
+    and visualize `iEEG` data from different perspectives.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.1.1
-Authors@R: 
-    person(given = "Zhengjia",
-           family = "Wang",
-           role = "cre",
-           email = "[email protected]")
+Authors@R: c(
+    person(given = "Zhengjia", family = "Wang", role = c("cre", "aut"), email = "[email protected]"),
+    person(given = "John", family = "Magnotti", role = "aut", email = "[email protected]")
+    )
 Imports:
+    methods,
+    stats,
+    graphics,
+    grid,
+    abind,
+    car,
+    utils,
+    data.table,
+    yaml (>= 2.2.0),
     shiny (>= 1.2.0),
     rlang (>= 0.3.0),
     stringr (>= 1.3.1),
-    magrittr,
-    circular,
-    lmerTest,
-    methods,
+    threeBrain (>= 0.1.3),
+    future (>= 0.14.0),
+    magrittr (>= 1.5),
+    circular (>= 0.4-93),
+    lmerTest (>= 3.1-0),
+    knitr,
+    assertthat,
+    shinyjs,
+    shinyFiles,
+    reshape2,
+    digest,
+    DT,
+    fst,
+    htmltools,
     rave,
-    rutabaga,
-    future,
-    abind,
-    stats
+    rutabaga
 Suggests:
     devtools,
-    yaml (>= 2.2.0),
     rstudioapi (>= 0.9.0)
 Remotes:
     github::dipterix/rutabaga,
-    github::dipterix/threeBrain,
     github::beauchamplab/rave

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+export(across_electrodes_beta_histogram)
+export(across_electrodes_f_histogram)
 export(by_condition_welch)
 export(by_trial_erp_map)
 export(dev_ravebuiltins)
@@ -16,15 +18,22 @@ import(rlang)
 import(rutabaga)
 import(shiny)
 import(stringr)
+importFrom(grDevices,col2rgb)
+importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,palette)
 importFrom(grDevices,pdf)
+importFrom(grDevices,rgb)
+importFrom(magrittr,"%$%")
 importFrom(magrittr,"%<>%")
 importFrom(magrittr,"%>%")
 importFrom(magrittr,extract)
 importFrom(magrittr,extract2)
+importFrom(methods,getMethod)
 importFrom(methods,is)
 importFrom(stats,median)
 importFrom(stats,median.default)
+importFrom(stats,p.adjust)
 importFrom(stats,pt)
 importFrom(stats,quantile)
+importFrom(stats,symnum)

R/aaa.R

@@ -6,25 +6,59 @@
 #' @importFrom magrittr %>%
 #' @import stringr
 #' @importFrom magrittr %<>%
+#' @importFrom magrittr %$%
 #' @importFrom magrittr extract2
 #' @importFrom magrittr extract
 #' @import rlang
 #' @import lmerTest
 #'
 #' @importFrom methods is
+#' @importFrom methods getMethod
 #' @import circular
 #' 
 #' @importFrom grDevices dev.off
 #' @importFrom grDevices pdf
 #' @importFrom grDevices palette
+#' @importFrom grDevices col2rgb
+#' @importFrom grDevices colorRampPalette
+#' @importFrom grDevices rgb
 #' 
 #' @import graphics
 #' 
 #' @importFrom stats median
 #' @importFrom stats median.default
 #' @importFrom stats pt
 #' @importFrom stats quantile
+#' @importFrom stats p.adjust
+#' @importFrom stats symnum
 #' 
+NULL
+
+# Add global variables to pass check
+..async_quo = NULL
+..async_var = NULL
+.palettes = NULL
+BASELINE = NULL
+FREQUENCY = NULL
+Frequency = NULL
+TIME_RANGE = NULL
+Time = NULL
+draw_time_baseline = NULL
+is_clean = NULL
+label.col = NULL
+x = NULL
+xax = NULL
+xlab = NULL
+y = NULL
+yax = NULL
+ylab = NULL
+data = NULL
+
+
+
+
+
+
 
 cat2 <- function(..., end = '\n', level = 'DEBUG', print_level = FALSE, pal = list(
     'DEBUG' = 'grey60',
@@ -262,14 +296,16 @@ rave_color_ramp_dark_palette <- colorRampPalette(c('#13547a', 'black', '#ff758c'
 ..dark_blue_to_red <- rev(c("#67001f", "#b2182b", "#d6604d", "#f4a582", "#fddbc7", "#ffffff", 
                         "#d1e5f0", "#92c5de", "#4393c3", "#2166ac", "#053061"))
 ..light_blue_to_light_red <- c(..dark_blue_to_red[5:1], 'black', ..dark_blue_to_red[11:7])
-
+..light_blue_to_gray_to_light_red <- c(..dark_blue_to_red[5:1], '#1E1E1E', ..dark_blue_to_red[11:7])
 
 rave_color_ramp_palette <- colorRampPalette(..dark_blue_to_red, interpolate='linear', space='Lab')
 rave_heat_map_colors <- rave_color_ramp_palette(1001)
 
 rave_color_ramp_dark_palette <- colorRampPalette(..light_blue_to_light_red, interpolate='linear', space='Lab')
+rave_color_ramp_gray_palette <- colorRampPalette(..light_blue_to_gray_to_light_red, interpolate='linear', space='Lab')
 
 rave_heat_map_dark_colors <- rave_color_ramp_dark_palette(1001)
+rave_heat_map_gray_colors <- rave_color_ramp_gray_palette(1001)
 
 # put this here for legacy, but we need to exterminate these references
 crp <- rave_heat_map_colors
@@ -282,12 +318,7 @@ rave_axis <- function(side, at, tcl=-0.3, labels=at, las=1, cex.axis=rave_cex.ax
 
   # if the color isn't specified, then we are free to set the color to what we want.
   # let's set it to be black, unless that background color is black, then we'll do white
-  col %?<-% if(par('bg') == 'black') {
-    'white'
-  } else {
-    'black'
-  }
-
+  col %?<-% get_foreground_color()
   col.axis %?<-% col
 
   ruta_axis(
@@ -305,8 +336,6 @@ rave_axis <- function(side, at, tcl=-0.3, labels=at, las=1, cex.axis=rave_cex.ax
   )
 }
 
-
-
 default_plot <- function() {
   plot_clean(1, 1, type='n', main='No Conditions Specified')
 }
@@ -387,11 +416,14 @@ rave_colors <- list('BASELINE_WINDOW'='gray60', 'ANALYSIS_WINDOW' = 'salmon2', '
                     'TRIAL_TYPE_SEPARATOR'='gray40')
 
 rave_title <- function(main, cex=rave_cex.main, col, font=1) {
-
-  col %?<-% if(par('bg') == 'black') {
-    'white'
-  } else {
-    'black'
+  if(missing(col)) {
+    col = if(par('bg') == 'black') {
+      'white'
+    } else if (par('bg') == '#1E1E1E'){
+      'gray70'
+    } else {
+      'black'
+    }
   }
 
   title(main=list(main, cex=cex, col=col, font=font))