In ningzhibin/rmdocpu: Metalab report upon provided templates

knitr::opts_chunk$set(echo = FALSE,warning = FALSE, message = FALSE, cache = FALSE)
library(canvasXpress)

  # y=read.table("http://www.canvasxpress.org/data/cX-heatmapR-dat.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
  # x=read.table("http://www.canvasxpress.org/data/cX-heatmapR-smp.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
  # z=read.table("http://www.canvasxpress.org/data/cX-heatmapR-var.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
  # 
  # 
  # canvasXpress(
  #   graphType="Heatmap",
  #   data=y,
  #   smpAnnot=x,
  #   varAnnot=z,
  #   
  #   
  #   colorSpectrumZeroValue = 0,
  #   colorSpectrum=list("magenta", "blue", "black","red", "gold"),
  #   
  #   
  #   # for color bar
  #   heatmapIndicatorWidth = 100, # for the color bar
  #   heatmapIndicatorHeight = 30,
  #   heatmapIndicatorHistogram = TRUE,
  #   
  #   heatmapIndicatorPosition ="topLeft",
  #   colorSpectrum=list("blue", "yellow", "red"),
  #   #colorSpectrumBreaks =list(8, 9,10),
  #   
  #   # for overlay sample grouping
  #   smpOverlays =list("Treatment","Site","Dose"),
  #   smpOverlayProperties=list(Dose=list(position="right", thickness=50, type="Bar"), Site=list(position="left"), Treatment=list(position="right")),
  #   
  #   # name the color for the grouping
  #   colorKey=list(Sens=list("white", "green"), Site="Pastel1", Treatment="Accent", Type="YlGn"),
  #   
  #   # sample grouping separation, se
  #   heatmapSmpSeparateBy = "Treatment",
  #   
  #   # for overlay of varabile grouping
  #   
  #   # higlight variable
  #    highlightVar=list("Probe18","Probe19","Probe20"),
  # 
  #   
  #   heatmapCellBoxColor="rgb(255,255,255)",
  #   samplesClustered=TRUE,
  #   showTransition=TRUE,
  #   title="Clustered data",
  #   variablesClustered=TRUE,
  #   width = 800, 
  #   height = 600
  # )
  # 
  # 
  # 
  # canvasXpress(
  #   data=y,
  #   smpAnnot=x,
  #   varAnnot=z,
  #   
  #   colorKey=list(Sens=list("white", "green"), Site="Pastel1", Treatment="Accent", Type="YlGn"),
  #   colorSpectrum=list("magenta", "blue", "black", "red", "gold"),
  #   colorSpectrumZeroValue=0,
  #   
  #   graphType="Heatmap",
  #   title="Advanced Overlays in Heatmaps",
  #   
  #   
  #   heatmapIndicatorHeight=50,
  #   heatmapIndicatorHistogram=TRUE,
  #   heatmapIndicatorPosition="topLeft",
  #   heatmapIndicatorWidth=60,
  #   
  #   samplesClustered=TRUE,
  #   variablesClustered=TRUE,
  #   showTransition=FALSE,
  #   
  #   
  #   smpOverlayProperties=list(Dose=list(position="right", thickness=50, type="Bar"), Site=list(position="left"), Treatment=list(position="right")),
  #   
  #   smpOverlays=list("Treatment", "Site", "Dose"),
  #   
  #   varOverlays=list("Type", "Sens"),
  #   varOverlayProperties=list(Sens=list(color="red", position="bottom", thickness=20, type="Bar"), Type=list(position="top")),
  #   
  # )




####

# y=read.table("http://www.canvasxpress.org/data/cX-overlays-dat.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
#   x=read.table("http://www.canvasxpress.org/data/cX-overlays-smp.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
#   z=read.table("http://www.canvasxpress.org/data/cX-overlays-var.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
#  
#   
#   canvasXpress(
#     data=y,
#     smpAnnot=x,
#     varAnnot=z,
#     graphType="Heatmap",
#     showTransition=FALSE,
#     smpLabelScaleFontFactor=1.1,
#     smpOverlayProperties=list(Binary=list(position="left", scheme="BlackAndWhite", type="Default"), Boolean=list(position="left"), Continuous=list(position="left", spectrum=list("green", "white"), type="Heatmap"), Discrete=list(position="left", thickness=30, type="Default"), Early=list(color="blue", position="right", thickness=50, type="Line"), Late=list(color="red", position="right", thickness=50, type="Line"), OnTime=list(color="green", position="right", thickness=50, type="Line"), PhaseA=list(position="left", thickness=50, type="Bar"), PhaseB=list(position="left", thickness=50, type="Bar"), PhaseC=list(position="left", thickness=50, type="Bar"), Temp=list(position="right", spectrum=list("blue", "white", "red"), thickness=100, type="Heatmap")),
#     smpOverlays=list("PhaseA", "PhaseB", "PhaseC", "-", "-", "Binary", "Boolean", "Continuous", "Discrete", "-", "-", "Temp", "-", "-", "Early", "OnTime", "Late"),
#     varLabelRotate=45,
#     varLabelScaleFontFactor=1.7,
#     varOverlayProperties=list(Cold=list(color="blue", position="bottom", thickness=50, type="StackedPercent"), Conc=list(position="top", thickness=40, type="Bar"), Desc=list(position="bottom", type="Text"), Drug=list(position="top", thickness=30, type="Increase"), Even=list(position="bottom", thickness=50, type="Bar"), Female=list(position="top", thickness=50, type="Pie"), Hot=list(color="red", position="bottom", thickness=50, type="StackedPercent"), Male=list(position="top", thickness=50, type="Pie"), Nice=list(color="green", position="bottom", thickness=50, type="Dotplot"), Odd=list(position="bottom", thickness=50, type="BarLine"), Site=list(position="top", type="Default"), Ugly=list(color="black", position="bottom", thickness=50, type="Dotplot")),
#     varOverlays=list("Drug", "-", "Male", "Female", "-", "Site", "-", "Conc", "-", "Desc", "-", "Even", "Odd", "-", "-", "Nice", "Ugly", "-", "-", "Cold", "Hot")
#   )



z <- seq(-10, 10, 0.1)
x <- cos(z)
y <- sin(z)
threejs::scatterplot3js(x, y, z, color=rainbow(length(z)))

  # DT::datatable(mtcars)

# 
#  advanced_scatterplot(data_frame = mtcars,
#                      x_index = 1,# column index/location
#                      y_index = 3,# column index/location
# 
#                      point_shape_index = NULL, # column index/location
#                      point_shape_manual = c(15, 16, 17, 18),
# 
#                      point_color_index = NULL, # column index/location
#                      point_color_manual = rainbow(10), # if point_color_index is null, only use the first color, otherwise
#                      point_color_type = "group", # c("graidnet", "group"), if group, will force to factor
# 
#                      point_size_index = NULL,
#                      point_size_manual = 4, # will be overide by point_size_index
#                      point_alpha = 0.5,
# 
#                      overlay_polygon = FALSE,
#                      polygon_type =  "convex", # or "ellipse"
#                      polygon_index = NULL, # draw polygon overlap, will choose
#                      polygon_alpha = 0.5,
#                      ellipse_confidience = 0.95, # only works when ellipse is choose for polygon_type
#                      polygon_fill_color_manual = rainbow(10), # null means auto color, otherwise provide list of color values
# 
#                      label_text_index = 8, # to do this section
#                      label_color_index = 8,
#                      label_color_manual = rainbow(10)[2:3],
#                      label_size_index =  NULL,
#                      label_size_manual  = 4,
# 
#                      equal_xy = FALSE
# 
#                     )