ColorKeyboard.R

# Author: Benben Miao
# Email: benben.miao@outlook.com
# Rversion: 4.2.0
# Date: 2022-11-30

# -> 0. Install and Library
# install.packages(c("ggplot2", "ggsci"))
# devtools::install_github("sharlagelfand/ggkeyboard", ref = "main")
library(ggplot2)
library(ggsci)
library(ggkeyboard)
# <- 0. Install and Library

options (warn = -1)

# -> 1. File Read
# file_path = "data/HexbinHive/HexbinHive.txt"
# file_format = "txt"
# # "xlsx", "xls", "txt", "csv"
# 
# if (file_format == "xlsx" | file_format == "xls") {
#     data <- readxl::read_excel(path = file_path,
#                                sheet = NULL,
#                                col_names = TRUE,
#                                na = "",
#                                progress = readxl::readxl_progress()
#     )
# } else if (file_format == "txt" | file_format == "csv") {
#     data <- read.table(file = file_path,
#                        header = TRUE,
#                        sep = "\t",
#                        stringsAsFactors = F
#     )
# } else if (file_format == "csv") {
#     data <- read.table(file = file_path,
#                        header = TRUE,
#                        sep = ",",
#                        stringsAsFactors = F
#     )
# }
# <- 1. File Read

# -> 2. Data Operation
# set.seed(123)
# df <- data.frame(x = rnorm(2000), y = rnorm(2000))
# write.table(df, "HexbinHive.txt", quote = F, sep = "\t", row.names = F)
# <- 2. Data Operation

# -> 3. Plot Parameters
fonts <- "Times"
# ChoiceBox: "Times", "Palatino", "Bookman", "Courier", "Helvetica", "URWGothic", "NimbusMon", "NimbusSan"

ggTheme <- "theme_light"
# ChoiceBox: "theme_default", "theme_bw", "theme_gray", "theme_light", "theme_linedraw", "theme_dark", "theme_minimal", "theme_classic", "theme_void"
if (ggTheme == "theme_default") {
    gg_theme <- theme()
} else if (ggTheme == "theme_bw") {
    gg_theme <- theme_bw()
} else if (ggTheme == "theme_gray") {
    gg_theme <- theme_gray()
} else if (ggTheme == "theme_light") {
    gg_theme <- theme_light()
} else if (ggTheme == "theme_linedraw") {
    gg_theme <- theme_linedraw()
} else if (ggTheme == "theme_dark") {
    gg_theme <- theme_dark()
} else if (ggTheme == "theme_minimal") {
    gg_theme <- theme_minimal()
} else if (ggTheme == "theme_classic") {
    gg_theme <- theme_classic()
} else if (ggTheme == "theme_void") {
    gg_theme <- theme_void()
} else if (ggTheme == "theme_test") {
    gg_theme <- theme_test()
}

sciFillAlpha <- 0.80
sciColorAlpha <- 0.80
sciFillColor <- "Sci_NPG"
# ChoiceBox: "Sci_AAAS", "Sci_NPG", "Sci_Simpsons", "Sci_JAMA", "Sci_GSEA", "Sci_Lancet", "Sci_Futurama", "Sci_JCO", "Sci_NEJM", "Sci_IGV", "Sci_UCSC", "Sci_D3", "Sci_Material"
if (sciFillColor == "Default"){
    sci_fill <- NULL
    sci_color <- NULL
} else if (sciFillColor == "Sci_AAAS") {
    sci_fill <- scale_fill_aaas(alpha = sciFillAlpha)
    sci_color <- scale_color_aaas(alpha = sciColorAlpha)
    # Science and Science Translational Medicine:
} else if (sciFillColor == "Sci_NPG") {
    sci_fill <- scale_fill_npg(alpha = sciFillAlpha)
    sci_color <- scale_color_npg(alpha = sciColorAlpha)
} else if (sciFillColor == "Sci_Simpsons") {
    sci_fill <- scale_fill_simpsons(alpha = sciFillAlpha)
    sci_color <- scale_color_simpsons(alpha = sciColorAlpha)
    # The Simpsons
} else if (sciFillColor == "Sci_JAMA") {
    sci_fill <- scale_fill_jama(alpha = sciFillAlpha)
    sci_color <- scale_color_jama(alpha = sciColorAlpha)
    # The Journal of the American Medical Association
} else if (sciFillColor == "Sci_Lancet") {
    sci_fill <- scale_fill_lancet(alpha = sciFillAlpha)
    sci_color <- scale_color_lancet(alpha = sciColorAlpha)
    #  Lancet Oncology
} else if (sciFillColor == "Sci_Futurama") {
    sci_fill <- scale_fill_futurama(alpha = sciFillAlpha)
    sci_color <- scale_color_futurama(alpha = sciColorAlpha)
    # Futurama
} else if (sciFillColor == "Sci_JCO") {
    sci_fill <- scale_fill_jco(alpha = sciFillAlpha)
    sci_color <- scale_color_jco(alpha = sciColorAlpha)
    # Journal of Clinical Oncology: 
} else if (sciFillColor == "Sci_NEJM") {
    sci_fill <- scale_fill_nejm(alpha = sciFillAlpha)
    sci_color <- scale_color_nejm(alpha = sciColorAlpha)
    # The New England Journal of Medicine
} else if (sciFillColor == "Sci_IGV") {
    sci_fill <- scale_fill_igv(alpha = sciFillAlpha)
    sci_color <- scale_color_igv(alpha = sciColorAlpha)
    # Integrative Genomics Viewer (IGV)
} else if (sciFillColor == "Sci_UCSC") {
    sci_fill <- scale_fill_ucscgb(alpha = sciFillAlpha)
    sci_color <- scale_color_ucscgb(alpha = sciColorAlpha)
    # UCSC Genome Browser chromosome sci_fill
} else if (sciFillColor == "Sci_D3") {
    sci_fill <- scale_fill_d3(alpha = sciFillAlpha)
    sci_color <- scale_color_d3(alpha = sciColorAlpha)
    # D3.JS
} else if (sciFillColor == "Sci_Material") {
    sci_fill <- scale_fill_material(alpha = sciFillAlpha)
    sci_color <- scale_color_material(alpha = sciColorAlpha)
    # The Material Design color palettes
}

title <- "Hexbin Hive"
# TextField

xlab <- colnames(data)[1]
ylab <- colnames(data)[2]

keyboardType <- "Tenkeyless"
# ChoiceBox: "Tenkeyless", "Mac", "Full", "SixtyPercent"
if (keyboardType == "Tenkeyless") {
    keyboard <- tkl
} else if (keyboardType == "Full") {
    keyboard <- full
} else if (keyboardType == "SixtyPercent") {
    keyboard <- sixty_percent
} else if (keyboardType == "Mac") {
    keyboard <- mac
}

keyboardPalette <- "pastel"
# ChoiceBox: "pastel", "serika", "wahtsy", "cyberpunk", "magic", "varmilo", "t0mb3ry"

layout <- "ansi"
# "ansi", "iso"

keyTextSize <- 3
# Slider: 3, 0, 10, 1


plotTitleFace <- "bold"
# ChoiceBox: "plain", "italic", "bold", "bold.italic"

plotTitleSize <- 18
# Slider: 18, 0, 50, 1

plotTitleHjust <- 0.5
# Slider: 0.5, 0.0, 1.0, 0.1

axisTitleFace <- "bold"
# ChoiceBox: "plain", "italic", "bold", "bold.italic"

axisTitleSize <- 14
# Slider: 16, 0, 50, 1

axisTextSize <- 10
# Slider: 10, 0, 50, 1

legendTitleSize <- 12
# Slider: 12, 0, 50, 1

legendPosition <- "right"
# ChoiceBox: "none", "left", "right", "bottom", "top"

legendDirection <- "vertical"
# ChoiceBox: "horizontal", "vertical"
# <- 3. Plot Parameters

# # -> 4. Plot
p <- ggkeyboard(keyboard = keyboard,
                # tkl, full, sixty_percent, mac
                palette = keyboard_palette(keyboardPalette),
                # c("pastel", "serika", "wahtsy", "cyberpunk", "magic", "varmilo", "t0mb3ry")
                layout = layout,
                # "ansi", "iso"
                font_family = fonts,
                font_size = keyTextSize,
                adjust_text_colour = TRUE,
                measurements = keyboard_measurements("default")
                ) 
    # %>%
    # highlight_keys(c("A", "W", "S", "D"),
    #                colour = "#ff000088",
    #                fill = "#ff000055"
    #                )

# # <- 4. Plot

# -> 5. Save parameters
pdf_name = "results.pdf"
jpeg_name = "results.jpeg"
device_pdf = "pdf" 
device_jpeg = "jpeg" 
# "pdf", "jpeg", "tiff", "png", "bmp", "svg" 
width = 10.0
height = 6.18
units = "in" 
# "in", "cm", "mm", "px" 
dpi <- 300 
# <- 5. Save parameters

# -> 6. Save Image
ggsave( 
    filename = pdf_name, 
    plot = p, 
    device = device_pdf, 
    path = NULL, 
    scale = 1, 
    width = width, 
    height = height, 
    units = units, 
    dpi = 300, 
    limitsize = TRUE 
) 
ggsave( 
    filename = jpeg_name, 
    plot = p, 
    device = device_jpeg, 
    path = NULL, 
    scale = 1, 
    width = width, 
    height = height, 
    units = units, 
    dpi = 300, 
    limitsize = TRUE 
)
# <- 6. Save Image