two_genomes_plot: Creation of non-circular two genomes plots

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

Description

The function to 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 dataset to define the genome aligned along the horizontal axis.
data.chr2	The dataset to define the genome aligned along the vertical axis.
data.2geno.plot	The main dataset used to create the two genomes plot.
theme_sty	Choose one figure theme from the following list: "theme1", "theme2", "theme3", "theme4", "theme5", "theme6", "theme7", "theme8", "theme9", "theme10", "theme11", "theme12", "theme13", "theme14", "theme15", "theme16", "theme17" and "theme18".
font_size	An integer number to set the font size.
xtitle	X axis title.
ytitle	Y axis title.
title_font_face	Font face of figure title, for example "plain", "italic", "bold" or "bold.italic".
xlabel	Show or hide tick labels on the X-axis. "1" to show, "2" to "hide".
ylabel	Show or hide tick labels on the Y-axis. "1" to show, "2" to "hide".
lgd_pos	The position to place the legend. "1" for "right", "2" for "bottom".
lgd_title_size	An integer number to set the font size of legend title.
lgd_title_font_face	The font face of legend title, for example "plain", "italic", "bold" or "bold.italic".
lgd_text_size	An integer number to set the font size of legend tick label.
lgd_text_font_face	The font face of legend tick label, for example "plain", "italic", "bold" or "bold.italic".
plot_type	Acceptable plot type can be "point_gradual", "point_discrete", "segment" , "rect_gradual" and "rect_discrete".
sel_gral_col	Data color for plot_type 'point_gradual' or 'rect_gradual'. By default, this parameter was set as "1" and predefined color would be used. If this parameter was set as "2", "low-high" gradient color would be used. If this parameter was set as "3", "low-mid-high" gradient color would be used.
gral_col_tp	If sel_gral_col was set as "1", choose 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", please provide two color values representing the low and the high color, for example "#0016DB" and "#FFFF00".
gral_3cols_ct	If sel_gral_col was set as "3", please provide three color values representing the low, the mid and the high color, for example "#0016DB", "#FFFFFF" and "#FFFF00".
col_type	Data color for plot_type 'point_discrete', 'segment' or 'rect_discrete'. By default, this parameter was set as "1" and random assigned color would be used. To customize a single color for the data, set this parameter as "2". To assign different colors for differing data groups, set this parameter as "2" and provide a "color" column in the input data to indicate 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 as "2", a specific color should be specified using this parameter, for example "#FF0000".
color_mulgp	If col_type was set as "3"", users should provide a character string like "a:red;b:blue;c:cyan" to assign colors to each group .
col_transpt	A decimal number in [0, 1] to adjust the color transparency. The higher the value, the deeper the color.
symbol_point	Symbol used for different points for plot_type "point_gradual" or "point_discrete". 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 as "2", the uploaded data should include a "shape" column composed of a categorical character vector.
point_size	Numeric value used to set the point size for plot_type "point_gradual" or "point_discrete". 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 composed of a categorical character vector.
line_size	Numeric value used to set the line width for plot_type "segment".
vertical	Create a set of vertical lines across the X-axis to separate different chromosomes. "1" means "show", while "2" means "hide".
vertical_col	Color of the vertical lines, for example "#000000".
vertical_size	Line width of the vertical lines, for example 0.2.
vertical_type	Line type of the vertical lines, for example "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	Color of the horizontal lines, for example horizontal_col="#000000".
horizontal_size	Line width of the horizontal lines, for example horizontal_size=0.2.
horizontal_type	Line type of the horizontal lines, for example "solid", "dashed", "dotted", "dotdash", "longdash" or "twodash".
add_border	Add borders to the rect grids, which can be used to separate different cells of the rect from each other. "1" means "add cell borders", while "2" means "not add".
border_col	Borders color. If add_border was set as "1", a specific color should be specified by the users, for example "#000000".
linetype	The line type to be used to plot the data, when plot_type was set as "segment", for example "solid", "dashed", "dotted", "dotdash", "longdash" or "twodash".
col_lgd	Sow (or not) the color legend in the plotting region. "1" means "show", while "2" means "hide".
col_lgd_name	Title of the color legend. Null value will result in an empty title.
col_lgd_mdy_label	Modify (or not) the labels of different colors in the color legend, when col_lgd was set as "1" and plot_type was set as "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 as "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	Show (or not) the size legend in the plotting region for plot_type "point". "1" means "show", while "2" means "hide".
size_lgd_name	Title of the size legend, when size_lgd was set as "1", for example "size". Null value will result in an empty title.
size_lgd_mdy_label	Modify (or not) the labels of legend in size legend, when size_lgd was set as "1" and plot_type was set as "point_gradual" or "point_discrete". "1" means "modify labels", while "2" means "not modify".
size_lgd_label	If size_lgd_mdy_label was set as "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	Show (or not) the shape legend in the plotting region for plot_type "point". "1" means "show", while "2" means "hide".
shape_lgd_name	Title of the shape legend, when shape_lgd was set as "1", for example "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 as "1" and plot_type was set as "point_gradual" or "point_discrete". "1" means "modify labels", while "2" means "not modify".
shape_lgd_label	If shape_lgd_mdy_label was set as "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")

venyao/shinyChromosomeR documentation built on June 10, 2019, 11:33 a.m.