two_genomes_plot: Creation of non-circular two genomes plots

In yimingfish/shinyChromosomeR: the R package for shinyChromosome, an Shiny application for interactive creation of non-circular whole genome diagram

Description

The function create two genomes plots for comparison of data across two genomes.

Usage

two_genomes_plot(data.chr1="", data.chr2="", data.2geno.plot="",
                theme_sty="theme1", font_size=16,
                xtitle="Genomic position 1", ytitle="Genomic position 2",
                title_font_face="plain", xlabel=1, ylabel=1, lgd_pos=1,
                lgd_title_size=12, lgd_title_font_face="plain", lgd_text_size=10,
                lgd_text_font_face="plain", plot_type="point_gradual", sel_gral_col=1,
                gral_col_tp="blue.white.red", gral_2cols_ct=c("#0016DB", "#FFFF00"),
                gral_3cols_ct=c("#0016DB", "#FFFFFF", "#FFFF00"),
                col_type=1, color_cus="#FF0000", color_mulgp="a:red;b:blue;c:cyan",
                col_transpt=1, symbol_point=16, symbol_point_type=1, point_size=0.8,
                point_size_type=1, line_size=0.2, vertical=2, vertical_col="#000000",
                vertical_size=0.2, vertical_type="solid", horizontal=2,
                horizontal_col="#000000", horizontal_size=0.2, horizontal_type="solid",
                add_border=2, border_col="#000000", linetype="solid", col_lgd=2,
                col_lgd_name="color", col_lgd_mdy_label=2, col_lgd_label="a,b,c",
                size_lgd=2, size_lgd_name="size", size_lgd_mdy_label=2, size_lgd_label="a,b,c",
                shape_lgd=2, shape_lgd_name="symbol", shape_lgd_mdy_label=2,
                shape_lgd_label="a,b,c")

Arguments

data.chr1	The first dataset defines the genome aligned along the horizontal axis.
data.chr2	The second dataset defines the genome aligned along the vertical axis.
data.2geno.plot	The third dataset is the main dataset used to create the two genomes plot.
theme_sty	Select one figure theme from themes list as "theme1", "theme2", "theme3", "theme4", "theme5", "theme6", "theme7", "theme8", "theme9", "theme10", "theme11", "theme12", "theme13", "theme14", "theme15", "theme16", "theme17" and "theme18".
font_size	Font size, like 16.
xtitle	X axis title, like "Genomic position 1".
ytitle	Y axis title, like "Genomic position 2".
title_font_face	Font face, like "plain", "italic", "bold" or "bold.italic".
xlabel	Show or hide tick labels on the X-axis. "1" means "show", while "2" means "hide".
ylabel	Show or hide tick labels on the Y-axis. "1" means "show", while "2" means "hide".
lgd_pos	The position to place the legend. "1" means "right", while "2" means "bottom".
lgd_title_size	The font size of legend title, like 12.
lgd_title_font_face	The font face of legend title, like "plain", "italic", "bold" or "bold.italic".
lgd_text_size	The font size of legend tick label, like 10.
lgd_text_font_face	The font face of legend tick label, like "plain", "italic", "bold" or "bold.italic".
plot_type	Select one plot type from list "point_gradual", "point_discrete", "segment" , "rect_gradual" and "rect_discrete".
sel_gral_col	If plot_type was set 'point_gradual' or 'rect_gradual'", colors to be used to plot the data. By default, this parameter was set as "1" and predefined color would be used. If the option was set as "2", color gradient is created as "low-high" pattern. If the option was set as "3", color gradient is created as "low-mid-high" pattern.
gral_col_tp	If sel_gral_col was set "1", select one data color from the following list: "blue.white.red", "green.black.red", "green.yellow.red", "purple.yellow.red", "blue.green.red", "blue.yellow.green", "cyan.white.deeppink1".
gral_2cols_ct	If sel_gral_col was set as "2", low-high color to be used for the data, like 'c("#0016DB", "#FFFF00")'.
gral_3cols_ct	If sel_gral_col was set as "3", low-mid-high color to be used for the data like 'c("#0016DB", "#FFFFFF", "#FFFF00")'.
col_type	If plot_type was set 'point_discrete', 'segment' or 'rect_discrete'", the color to be used to plot the data. By default, this parameter was set as "1" and random assigned color would be used. To customize one color for data, users should choose a color from the color palette. To customize color for data with multiple groups, the column indicating different groups should be named as "color" in the input data. Users should provide a character string assigning colors to each group. For example, "a:red;b:green;c:blue", in which "a b c" represent different data groups. Color for data groups without assigned color would be set as "NA". Hex color codes as "#FF0000" are also supported. See example data for more details. "1" means "random", "2" means "one custom color" and "3" means "custom for data with multi-group".
color_cus	If "col_type" was set "2", a specific color should be specified using this option, like "#FF0000".
color_mulgp	If col_type was set as 3, users should provide a character string assigning colors to each group like "a:red;b:blue;c:cyan".
col_transpt	A decimal number in [0, 1] to adjust the color transparency like 1. The higher the value, the deeper the color.
symbol_point	If plot_type was set "point_gradual" or "point_discrete", symbol used for different points, like 16. Applicable values are integers in [0-25]. Check "http://www.endmemo.com/program/R/pchsymbols.php" for more details. A single integer can be used to set the shape of all points.
symbol_point_type	Symbol used for different points. By default, this parameter was set as "1" and one custom symbol would be used. If the option was set "2", the uploaded data should include a "shape" column with a categorical character vector.
point_size	If plot_type was set "point_gradual" or "point_discrete", value used for different size of points, like 0.8. A single numeric value can be used to set the size of all points.
point_size_type	Value used for different size of points. By default, this parameter was set as "1" and one custom symbol would be used. If the option was set "2", the uploaded data should include a "size" column with a categorical character vector.
line_size	If plot_type was set "segment", the line width to be used to plot the data, like 0.2.
vertical	Create a set of vertical lines across the X-axis to separate different chromosomes. "1" means "show", while "2" means "hide".
vertical_col	If vertical was set "1", color of the vertical lines, like "#000000".
vertical_size	If vertical was set "1", line width of the vertical lines, like 0.2.
vertical_type	If vertical was set "1", line type of the vertical lines, like "solid", "dashed", "dotted", "dotdash", "longdash" or "twodash".
horizontal	Create a set of horizontal lines across the Y-axis to separate different chromosomes. "1" means "show", while "2" means "hide".
horizontal_col	If horizontal was set "1", color of the horizontal lines, like horizontal_col="#000000".
horizontal_size	If horizontal was set "1", line width of the horizontal lines, like horizontal_size=0.2.
horizontal_type	If horizontal was set "1", line type of the horizontal lines, like "solid", "dashed", "dotted", "dotdash", "longdash" or "twodash".
add_border	Add borders to the rect grids, which can be used to separate cells from each other. "1" means "add cell borders", while "2" means "not add".
border_col	Borders color. If add_border was set "1", a specific color should be specified by the users, like "#000000".
linetype	The line type to be used to plot the data, when plot_type was set "segment", like "solid", "dashed", "dotted", "dotdash", "longdash" or "twodash".
col_lgd	Control the appearance of the color legend in the plotting region. "1" means "show", while "2" means "hide".
col_lgd_name	Title of the color legend, when col_lgd was set "1", like "color". Null value will result in an empty title.
col_lgd_mdy_label	The labels of different colors in the color legend, when col_lgd was set "1" and plot_type was set "point_discrete", "segment" or "rect_discrete". "1" means "modify labels", while "2" means "not modify".
col_lgd_label	If col_lgd_mdy_label was set "1", character vector of arbitrary length is accepted and adjusted automatically to the number of groups, which is separated by commas. For example, "a" or "a,b,c".
size_lgd	If plot_type was set "point", control the appearance of the size legend in the plotting region. "1" means "show", while "2" means "hide".
size_lgd_name	Title of the size legend, when size_lgd was set "1", like "size". Null value will result in an empty title.
size_lgd_mdy_label	The labels of legend in size legend, when size_lgd was set "1" and plot_type was set "point_gradual" or "point_discrete". "1" means "modify labels", while "2" means "not modify".
size_lgd_label	If size_lgd_mdy_label was set "1", character vector of arbitrary length is accepted and adjusted automatically to the number of groups, which is separated by commas. For example, "a" or "a,b,c".
shape_lgd	If plot_type was set "point", control the appearance of the shape legend in the plotting region. "1" means "show", while "2" means "hide".
shape_lgd_name	Title of the shape legend, when shape_lgd was set "1", like "symbol". Null value will result in an empty title.
shape_lgd_mdy_label	The labels of legend in shape legend, when shape_lgd was set "1" and plot_type was set "point_gradual" or "point_discrete". "1" means "modify labels", while "2" means "not modify".
shape_lgd_label	If shape_lgd_mdy_label was set "1", character vector of arbitrary length is accepted and adjusted automatically to the number of groups, which is separated by commas. For example, "a" or "a,b,c".

Author(s)

Yiming Yu, Wen Yao

Examples

data.chr1 <- read.table(system.file("examples/two_genome/genome1_data.txt",
                  package="shinyChromosomeR"), header=TRUE, as.is=TRUE, sep="\t")
head(data.chr1)

data.chr2 <- read.table(system.file("examples/two_genome/genome2_data.txt",
                  package="shinyChromosomeR"), header=TRUE, as.is=TRUE, sep="\t")
head(data.chr2)

data.2geno.plot <- read.table(system.file("examples/two_genome/point_gradual.txt",
                        package="shinyChromosomeR"), header=TRUE, as.is=TRUE, sep="\t")
head(data.2geno.plot)

two_genomes_plot(data.chr1=data.chr1, data.chr2=data.chr2, data.2geno.plot=data.2geno.plot,
                plot_type="point_gradual")

yimingfish/shinyChromosomeR documentation built on Sept. 29, 2020, 5:46 p.m.