single_genome_plot: Creation of non-circular single genome plot
In yimingfish/shinyChromosomeR: the R package for shinyChromosome, an Shiny application for interactive creation of non-circular whole genome diagram
Description
Usage
Arguments
Author(s)
Examples
View source: R/single_genome_plot.R
Description
The function to create non-circular plot along all chromosomes of a single genome.
Usage
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single_genome_plot(data.chr="", data.track="", plot_type="point",
layer_index=paste0("track",1:length(plot_type)),
col_type=rep(1,length(plot_type)),
color_cus=rep("#FF0000",length(plot_type)),
color_mulgp=rep("a:red;b:blue;c:cyan",length(plot_type)),
col_transpt=rep(1,length(plot_type)),
add_border=rep(2,length(plot_type)),
border_col=rep("#000000",length(plot_type)),
rect_col=rep(1,length(plot_type)),
rect_col_dis=rep("#FF0000",length(plot_type)),
rect_col_dis_cus=rep("a:red;b:blue;c:cyan",length(plot_type)),
rect_grad_col=rep(1,length(plot_type)),
col_rect=rep("blue",length(plot_type)),
rect_grad_cus_2cols=rep("#0016DB.#FFFF00",length(plot_type)),
rect_grad_cus_3cols=rep("#0016DB.#FFFFFF.#FFFF00",length(plot_type)),
sel_heatmap_col=rep(1,length(plot_type)),
hmap_col=rep("blue.white.red",length(plot_type)),
heatmap_col_cus_2cols=rep("#0016DB.#FFFF00",length(plot_type)),
heatmap_col_cus_3cols=rep("#0016DB.#FFFFFF.#FFFF00",length(plot_type)),
hmap_col_dis=rep(1,length(plot_type)),
hmap_col_dis_cus=rep("a:red;b:blue;c:cyan",length(plot_type)),
sel_symbol_point=rep(1,length(plot_type)),
symbol_point=rep(16,length(plot_type)),
sel_point_size=rep(1,length(plot_type)),
point_size=rep(0.8,length(plot_type)),
line_color=rep("#FF0000",length(plot_type)),
line_size=rep(0.2,length(plot_type)),
fill_area=rep(2,length(plot_type)),
sel_area_type=rep(1,length(plot_type)),
border_area=rep("#0000FF",length(plot_type)),
linetype=rep("solid",length(plot_type)),
add_arrow=rep(2,length(plot_type)),
arrow_pos=rep(1,length(plot_type)),
arrow_size=rep(0.1,length(plot_type)),
text_col=rep("#000000",length(plot_type)),
text_size=rep(2,length(plot_type)),
font_face=rep("plain",length(plot_type)),
text_angle=rep(60,length(plot_type)),
col_lgd=rep(2,length(plot_type)),
col_lgd_name=rep("color",length(plot_type)),
col_lgd_mdy_label=rep(2,length(plot_type)),
col_lgd_label=rep("a,b,c",length(plot_type)),
size_lgd=rep(2,length(plot_type)),
size_lgd_name=rep("size",length(plot_type)),
size_lgd_mdy_label=rep(2,length(plot_type)),
size_lgd_label=rep("a,b,c",length(plot_type)),
shape_lgd=rep(2,length(plot_type)),
shape_lgd_name=rep("symbol",length(plot_type)),
shape_lgd_mdy_label=rep(2,length(plot_type)),
shape_lgd_label=rep("a,b,c",length(plot_type)),
line_type_lgd=rep(2,length(plot_type)),
line_type_lgd_name=rep("linetype",length(plot_type)),
line_type_lgd_mdy_label=rep(2,length(plot_type)),
line_type_lgd_label=rep("a",length(plot_type)),
lgd_pos=1, lgd_space_size=0.04, lgd_intra_size=40,
lgd_title_size=12, lgd_title_font_face="plain",
lgd_text_size=10, lgd_text_font_face="plain",
ylabel=rep(1,length(plot_type)),
height_layer=rep(0.06,length(plot_type)),
margin_layer=rep(0.01,length(plot_type)),
chr_plotype=1, plot_direct=1, theme_sty="theme1",
font_size=16, xtitle="Genomic position",
ytitle="Value", title_font_face="plain", xlabel=1)
Arguments
data.chr
The name of a compulsory genome dataset to define the frame of a non-circular plot.
data.track
The name of one or more datasets to be displayed along all chromosomes
of the input genome as different types of plots in one or more tracks.
plot_type
The plot types for different uploaded datasets, which should be chosen from the following list:
"point", "line", "bar", "rect_gradual", "rect_discrete", "heatmap_gradual", "heatmap_discrete",
"text", "segment", "vertical_line", "horizontal_line" and "ideogram".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
layer_index
The track index for different uploaded datasets, which should be specified as "track1", c("track1", "track1") or c("track1", "track2").
The number of values received through this parameter should be equal to that of the values received through the data.track parameter.
col_type
The color to be used to plot the data, when plot_type should be chosen from the following list: 'point', 'line', 'bar' and 'segment'.
By default, this parameter was set as "1" and random assigned color would be used.
To customize one color for data, set this parameter as 2.
To customize color for data with multiple groups, set this parameter as 3.
And the column indicating different groups in the uploaded data should be named as "color".
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. The number of values received through this parameter
should be equal to that of the values received through the data.track parameter.
color_cus
If col_type was set as 2, a specific color should be specified using this option, like "#FF0000" or c("red", "blue").
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
color_mulgp
If col_type was set as 3, 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.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
col_transpt
A decimal number in [0, 1] to adjust the color transparency, like 1 or 0.5.
The higher the value, the deeper the color. The number of values received
through this parameter should be equal to that of the values
received through the data.track parameter.
add_border
Add borders to the grids, which can be used to separate cells from each other.
"1" means "add cell borders", while "2" means "not add".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
border_col
Borders color. If add_border was set "1", a specific color should be specified by the users, like "#000000".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
rect_col
The color to be used to plot the data, when plot_type was set "rect_discrete".
By default, this parameter was set as "1" and random assigned color would be used.
If the option was set as "2", all data will be filled by a specified color.
If the option was set as "3", the 4th column of the uploaded data should be a
categorical character vector with no more than 50 groups.
Users should provide values as "a:red;b:green;c:blue", in which "a b c" represent
different data categories indicated by the 4th column of the uploaded data.
Color for data without custom color will be set as NULL.
Hex color codes as "#FF0000" are also supported.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
rect_col_dis
If rect_col was set as "2", all data will be filled by a specified color by this parameter, like "#FF0000".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
rect_col_dis_cus
If rect_col was set as "3", the 4th column of the uploaded data should be
a categorical character vector with no more than 50 groups.
Users should provide values as "a:red;b:green;c:blue",
in which "a b c" represent different data categories indicated by
the 4th column of the uploaded data.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
rect_grad_col
Colors to be used for the data, when plot_type was set "rect_gradual".
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.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
col_rect
A color vector for gradual rectangles, when rect_grad_col is "1".
Every value of this vector should be chosen from the following list:
"blue", "red", "green", "cyan",
"purple", "pink", "orange", "yellow", "navy", "seagreen", "maroon",
"olivedrab", "gold", "lightblue", "navy.yellow", "purple.seagreen",
"navy.orange", "navy.cyan", "blue.red" and "green.red".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
rect_grad_cus_2cols
If rect_grad_col was set as "2", low-high color to be used for the data.
For example, "blue.red".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
rect_grad_cus_3cols
If rect_grad_col was set as "3", low-mid-high color to be used for the data.
For example, "blue.white.red".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
sel_heatmap_col
Colors to be used for the data, when plot_type was set "heatmap_gradual".
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.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
hmap_col
If sel_heatmap_col was set as "1", Select one color from color list as "blue.white.red", "green.black.red",
"green.yellow.red", "purple.yellow.red", "blue.green.red",
"blue.yellow.green" and "cyan.white.deeppink1".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
heatmap_col_cus_2cols
If sel_heatmap_col was set as "2", low-high color to be used for the data.
For example, "blue.red".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
heatmap_col_cus_3cols
If sel_heatmap_col was set as "3", low-mid-high color to be used for the data.
For example, "blue.white.red".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
hmap_col_dis
The color to be used to plot the data, when plot_type was set "heatmap_discrete".
By default, this parameter was set as "1" and random assigned color would be used.
If the option was set "2", the 4th column of the uploaded data should
be a categorical character vector with no more than 50 groups.
Users should provide values as "a:red;b:green;c:blue",
in which "a b c" represent different data categories indicated
by the 4th column of the uploaded data.
Color for data without custom color will be set as NULL.
Hex color codes as "#FF0000" are also supported.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
hmap_col_dis_cus
If hmap_col_dis was set "2", the 4th column of the uploaded data
should be a categorical character vector with no more than 50 groups.
Users should provide values as "a:red;b:green;c:blue",
in which "a b c" represent different data categories indicated by
the 4th column of the uploaded data.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
sel_symbol_point
Symbol used for different points, when plot_type was set "point".
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.
A single integer can be used to set the shape of all points or a integer
column named as "shape" in the input data can be used to
set the shape of different points.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
symbol_point
If sel_symbol_point was set "1", 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.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
sel_point_size
Value used for different size of points, when plot_type was set "point".
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.
A single numeric value can be used to set the size of all points or a numeric column named
as "size" in the input data can be used to set the size of different points.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
point_size
If sel_point_size was set "1", value used for different size of points, like 0.8.
A single numeric value can be used to set the size of all points.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
line_color
The color to be used to plot the data, when plot_type should be chosen from the following list: 'vertical_line' and 'horizontal_line', like "#FF0000".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
line_size
The line width to be used to plot the data, when plot_type should be chosen from the following list: "line", "vertical_line", "horizontal_line" and
"segment", like 0.2. The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
fill_area
Fill the area below the lines, when plot_type was set "line".
By default, this parameter was set as "2".
"1" means "fill the area", while "2" means "not fill".
sel_area_type
Color to be used to fill the area, which can be identical with lines
color or be specified by the users.
If the option was set "1", all data will be filled by the color identical with lines.
If the option was set "2", all data will be filled by a specified color as "blue".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
border_area
If sel_area_type was set as "2", all data will be filled by a specified color as "#0000FF".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
linetype
The line type to be used to plot the data, when plot_type should be chosen from the following list: "line", "vertical_line", "horizontal_line" and
"segment", like "solid", "dashed", "dotted", "dotdash", "longdash" and "twodash".
The line type is automatically set as "solid" for line with more than one color.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
add_arrow
If plot_type was set segment, add arrow head for the segment.
"1" means "add arrow head", while "2" means "not add arrow head".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
arrow_pos
The position of arrow head, when add_arrow was set "1".
"1" means "line end", while "2" means "line beginning".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
arrow_size
The size of arrow head, when add_arrow was set "1", like 0.1.
The number of values received through this parameter
should be equal to that of the values received through the data.track parameter.
text_col
If plot_type was set "text", the font color is valid, like "#000000".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
text_size
If plot_type was set "text", the text size is valid, like 2.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
font_face
If plot_type was set "text", the font face is valid, like "plain", "italic", "bold" and "bold.italic".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
text_angle
If plot_type was set "text", the text angle is valid, which is decimal number in [0, 360], like 60.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
col_lgd
Control the appearance of the color legend in the plotting region.
"1" means "show", while "2" means "hide".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
col_lgd_name
Title of the color legend, when col_lgd was set "1", like "color".
Null value will result in an empty title.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
col_lgd_mdy_label
The labels of different colors in the color legend, when col_lgd was set "1" and plot_type was not set "rect_gradual" or "heatmap_gradual".
"1" means "modify labels", while "2" means "not modify".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
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".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
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".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
size_lgd_name
Title of the size legend, when size_lgd was set "1", like "size".
Null value will result in an empty title.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
size_lgd_mdy_label
The labels of legend in size legend, when size_lgd was set "1" and plot_type was set "point".
"1" means "modify labels", while "2" means "not modify".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
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".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
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".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
shape_lgd_name
Title of the shape legend, when shape_lgd was set "1", like "symbol".
Null value will result in an empty title.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
shape_lgd_mdy_label
The labels of legend in shape legend, when shape_lgd was set "1" and plot_type was set "point".
"1" means "modify labels", while "2" means "not modify".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
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".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
line_type_lgd
If plot_type was set "vertical_line" or "horizontal_line",
control the appearance of the line type legend in the plotting region.
"1" means "show", while "2" means "hide".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
line_type_lgd_name
Title of the line type legend, when line_type_lgd was set "1", like "linetype".
Null value will result in an empty title.
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
line_type_lgd_mdy_label
The labels of legend in linetype legend, when line_type_lgd was set "1" and plot_type was set "vertical_line" or "horizontal_line".
"1" means "modify labels", while "2" means "not modify".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
line_type_lgd_label
If line_type_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".
The number of values received through this parameter should be
equal to that of the values received through the data.track parameter.
lgd_pos
The position to place the legend. "1" means "right", while "2" means "bottom".
lgd_space_size
Percent of legend size relative to the main plotting region.
Applicable values are numbers in [0-1], like 0.04.
lgd_intra_size
Intra-spacing between different legends, like 40.
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".
ylabel
Show or hide tick labels on the Y-axis.
"1" means "show", while "2" means "hide".
height_layer
Height of the track as 0.06. The number of values received through this parameter
should be equal to that of the values received through the data.track parameter.
margin_layer
Margin size of the track as 0.01. The number of values received through this parameter
should be equal to that of the values received through the data.track parameter.
chr_plotype
All chromosomes can either be concatenated or separated.
"1" means "Concatenated chromosomes", while "2" means "Separated chromosomes".
plot_direct
Chromosomes could be aligned to the horizontal axis or the vertical axis.
"1" means "Horizontally aligned", while "2" means "Vertically aligned".
theme_sty
Select one figure theme from themes list "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".
ytitle
Y axis title, like "Value".
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".
Author(s)
Yiming Yu, Wen Yao
Examples
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data.chr <- read.table(system.file("examples/single_genome/genome_data.txt",
package="shinyChromosomeR"), header=TRUE, as.is=TRUE, sep="\t")
head(data.chr)
data.track.file <- c(system.file("examples/single_genome/point.txt", package="shinyChromosomeR"),
system.file("examples/single_genome/line.txt", package="shinyChromosomeR"))
data.track.file
data.track <- lapply(data.track.file, function(x){
dt <- read.table(x, header=TRUE, as.is=TRUE, sep="\t")
return(dt)
})
single_genome_plot(data.chr=data.chr, data.track=data.track, plot_type=c("point", "line"))
yimingfish/shinyChromosomeR documentation built on Sept. 29, 2020, 5:46 p.m.
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Description Usage Arguments Author(s) Examples
View source: R/single_genome_plot.R
Description
The function to create non-circular plot along all chromosomes of a single genome.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 | single_genome_plot(data.chr="", data.track="", plot_type="point",
layer_index=paste0("track",1:length(plot_type)),
col_type=rep(1,length(plot_type)),
color_cus=rep("#FF0000",length(plot_type)),
color_mulgp=rep("a:red;b:blue;c:cyan",length(plot_type)),
col_transpt=rep(1,length(plot_type)),
add_border=rep(2,length(plot_type)),
border_col=rep("#000000",length(plot_type)),
rect_col=rep(1,length(plot_type)),
rect_col_dis=rep("#FF0000",length(plot_type)),
rect_col_dis_cus=rep("a:red;b:blue;c:cyan",length(plot_type)),
rect_grad_col=rep(1,length(plot_type)),
col_rect=rep("blue",length(plot_type)),
rect_grad_cus_2cols=rep("#0016DB.#FFFF00",length(plot_type)),
rect_grad_cus_3cols=rep("#0016DB.#FFFFFF.#FFFF00",length(plot_type)),
sel_heatmap_col=rep(1,length(plot_type)),
hmap_col=rep("blue.white.red",length(plot_type)),
heatmap_col_cus_2cols=rep("#0016DB.#FFFF00",length(plot_type)),
heatmap_col_cus_3cols=rep("#0016DB.#FFFFFF.#FFFF00",length(plot_type)),
hmap_col_dis=rep(1,length(plot_type)),
hmap_col_dis_cus=rep("a:red;b:blue;c:cyan",length(plot_type)),
sel_symbol_point=rep(1,length(plot_type)),
symbol_point=rep(16,length(plot_type)),
sel_point_size=rep(1,length(plot_type)),
point_size=rep(0.8,length(plot_type)),
line_color=rep("#FF0000",length(plot_type)),
line_size=rep(0.2,length(plot_type)),
fill_area=rep(2,length(plot_type)),
sel_area_type=rep(1,length(plot_type)),
border_area=rep("#0000FF",length(plot_type)),
linetype=rep("solid",length(plot_type)),
add_arrow=rep(2,length(plot_type)),
arrow_pos=rep(1,length(plot_type)),
arrow_size=rep(0.1,length(plot_type)),
text_col=rep("#000000",length(plot_type)),
text_size=rep(2,length(plot_type)),
font_face=rep("plain",length(plot_type)),
text_angle=rep(60,length(plot_type)),
col_lgd=rep(2,length(plot_type)),
col_lgd_name=rep("color",length(plot_type)),
col_lgd_mdy_label=rep(2,length(plot_type)),
col_lgd_label=rep("a,b,c",length(plot_type)),
size_lgd=rep(2,length(plot_type)),
size_lgd_name=rep("size",length(plot_type)),
size_lgd_mdy_label=rep(2,length(plot_type)),
size_lgd_label=rep("a,b,c",length(plot_type)),
shape_lgd=rep(2,length(plot_type)),
shape_lgd_name=rep("symbol",length(plot_type)),
shape_lgd_mdy_label=rep(2,length(plot_type)),
shape_lgd_label=rep("a,b,c",length(plot_type)),
line_type_lgd=rep(2,length(plot_type)),
line_type_lgd_name=rep("linetype",length(plot_type)),
line_type_lgd_mdy_label=rep(2,length(plot_type)),
line_type_lgd_label=rep("a",length(plot_type)),
lgd_pos=1, lgd_space_size=0.04, lgd_intra_size=40,
lgd_title_size=12, lgd_title_font_face="plain",
lgd_text_size=10, lgd_text_font_face="plain",
ylabel=rep(1,length(plot_type)),
height_layer=rep(0.06,length(plot_type)),
margin_layer=rep(0.01,length(plot_type)),
chr_plotype=1, plot_direct=1, theme_sty="theme1",
font_size=16, xtitle="Genomic position",
ytitle="Value", title_font_face="plain", xlabel=1)
|
Arguments
data.chr |
The name of a compulsory genome dataset to define the frame of a non-circular plot. |
data.track |
The name of one or more datasets to be displayed along all chromosomes of the input genome as different types of plots in one or more tracks. |
plot_type |
The plot types for different uploaded datasets, which should be chosen from the following list: "point", "line", "bar", "rect_gradual", "rect_discrete", "heatmap_gradual", "heatmap_discrete", "text", "segment", "vertical_line", "horizontal_line" and "ideogram". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
layer_index |
The track index for different uploaded datasets, which should be specified as "track1", c("track1", "track1") or c("track1", "track2"). The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
col_type |
The color to be used to plot the data, when plot_type should be chosen from the following list: 'point', 'line', 'bar' and 'segment'. By default, this parameter was set as "1" and random assigned color would be used. To customize one color for data, set this parameter as 2. To customize color for data with multiple groups, set this parameter as 3. And the column indicating different groups in the uploaded data should be named as "color". 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. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
color_cus |
If col_type was set as 2, a specific color should be specified using this option, like "#FF0000" or c("red", "blue"). The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
color_mulgp |
If col_type was set as 3, 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. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
col_transpt |
A decimal number in [0, 1] to adjust the color transparency, like 1 or 0.5. The higher the value, the deeper the color. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
add_border |
Add borders to the grids, which can be used to separate cells from each other. "1" means "add cell borders", while "2" means "not add". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
border_col |
Borders color. If add_border was set "1", a specific color should be specified by the users, like "#000000". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
rect_col |
The color to be used to plot the data, when plot_type was set "rect_discrete". By default, this parameter was set as "1" and random assigned color would be used. If the option was set as "2", all data will be filled by a specified color. If the option was set as "3", the 4th column of the uploaded data should be a categorical character vector with no more than 50 groups. Users should provide values as "a:red;b:green;c:blue", in which "a b c" represent different data categories indicated by the 4th column of the uploaded data. Color for data without custom color will be set as NULL. Hex color codes as "#FF0000" are also supported. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
rect_col_dis |
If rect_col was set as "2", all data will be filled by a specified color by this parameter, like "#FF0000". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
rect_col_dis_cus |
If rect_col was set as "3", the 4th column of the uploaded data should be a categorical character vector with no more than 50 groups. Users should provide values as "a:red;b:green;c:blue", in which "a b c" represent different data categories indicated by the 4th column of the uploaded data. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
rect_grad_col |
Colors to be used for the data, when plot_type was set "rect_gradual". 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. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
col_rect |
A color vector for gradual rectangles, when rect_grad_col is "1". Every value of this vector should be chosen from the following list: "blue", "red", "green", "cyan", "purple", "pink", "orange", "yellow", "navy", "seagreen", "maroon", "olivedrab", "gold", "lightblue", "navy.yellow", "purple.seagreen", "navy.orange", "navy.cyan", "blue.red" and "green.red". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
rect_grad_cus_2cols |
If rect_grad_col was set as "2", low-high color to be used for the data. For example, "blue.red". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
rect_grad_cus_3cols |
If rect_grad_col was set as "3", low-mid-high color to be used for the data. For example, "blue.white.red". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
sel_heatmap_col |
Colors to be used for the data, when plot_type was set "heatmap_gradual". 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. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
hmap_col |
If sel_heatmap_col was set as "1", Select one color from color list as "blue.white.red", "green.black.red", "green.yellow.red", "purple.yellow.red", "blue.green.red", "blue.yellow.green" and "cyan.white.deeppink1". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
heatmap_col_cus_2cols |
If sel_heatmap_col was set as "2", low-high color to be used for the data. For example, "blue.red". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
heatmap_col_cus_3cols |
If sel_heatmap_col was set as "3", low-mid-high color to be used for the data. For example, "blue.white.red". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
hmap_col_dis |
The color to be used to plot the data, when plot_type was set "heatmap_discrete". By default, this parameter was set as "1" and random assigned color would be used. If the option was set "2", the 4th column of the uploaded data should be a categorical character vector with no more than 50 groups. Users should provide values as "a:red;b:green;c:blue", in which "a b c" represent different data categories indicated by the 4th column of the uploaded data. Color for data without custom color will be set as NULL. Hex color codes as "#FF0000" are also supported. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
hmap_col_dis_cus |
If hmap_col_dis was set "2", the 4th column of the uploaded data should be a categorical character vector with no more than 50 groups. Users should provide values as "a:red;b:green;c:blue", in which "a b c" represent different data categories indicated by the 4th column of the uploaded data. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
sel_symbol_point |
Symbol used for different points, when plot_type was set "point". 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. A single integer can be used to set the shape of all points or a integer column named as "shape" in the input data can be used to set the shape of different points. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
symbol_point |
If sel_symbol_point was set "1", 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. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
sel_point_size |
Value used for different size of points, when plot_type was set "point". 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. A single numeric value can be used to set the size of all points or a numeric column named as "size" in the input data can be used to set the size of different points. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
point_size |
If sel_point_size was set "1", value used for different size of points, like 0.8. A single numeric value can be used to set the size of all points. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
line_color |
The color to be used to plot the data, when plot_type should be chosen from the following list: 'vertical_line' and 'horizontal_line', like "#FF0000". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
line_size |
The line width to be used to plot the data, when plot_type should be chosen from the following list: "line", "vertical_line", "horizontal_line" and "segment", like 0.2. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
fill_area |
Fill the area below the lines, when plot_type was set "line". By default, this parameter was set as "2". "1" means "fill the area", while "2" means "not fill". |
sel_area_type |
Color to be used to fill the area, which can be identical with lines color or be specified by the users. If the option was set "1", all data will be filled by the color identical with lines. If the option was set "2", all data will be filled by a specified color as "blue". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
border_area |
If sel_area_type was set as "2", all data will be filled by a specified color as "#0000FF". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
linetype |
The line type to be used to plot the data, when plot_type should be chosen from the following list: "line", "vertical_line", "horizontal_line" and "segment", like "solid", "dashed", "dotted", "dotdash", "longdash" and "twodash". The line type is automatically set as "solid" for line with more than one color. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
add_arrow |
If plot_type was set segment, add arrow head for the segment. "1" means "add arrow head", while "2" means "not add arrow head". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
arrow_pos |
The position of arrow head, when add_arrow was set "1". "1" means "line end", while "2" means "line beginning". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
arrow_size |
The size of arrow head, when add_arrow was set "1", like 0.1. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
text_col |
If plot_type was set "text", the font color is valid, like "#000000". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
text_size |
If plot_type was set "text", the text size is valid, like 2. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
font_face |
If plot_type was set "text", the font face is valid, like "plain", "italic", "bold" and "bold.italic". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
text_angle |
If plot_type was set "text", the text angle is valid, which is decimal number in [0, 360], like 60. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
col_lgd |
Control the appearance of the color legend in the plotting region. "1" means "show", while "2" means "hide". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
col_lgd_name |
Title of the color legend, when col_lgd was set "1", like "color". Null value will result in an empty title. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
col_lgd_mdy_label |
The labels of different colors in the color legend, when col_lgd was set "1" and plot_type was not set "rect_gradual" or "heatmap_gradual". "1" means "modify labels", while "2" means "not modify". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
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". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
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". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
size_lgd_name |
Title of the size legend, when size_lgd was set "1", like "size". Null value will result in an empty title. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
size_lgd_mdy_label |
The labels of legend in size legend, when size_lgd was set "1" and plot_type was set "point". "1" means "modify labels", while "2" means "not modify". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
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". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
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". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
shape_lgd_name |
Title of the shape legend, when shape_lgd was set "1", like "symbol". Null value will result in an empty title. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
shape_lgd_mdy_label |
The labels of legend in shape legend, when shape_lgd was set "1" and plot_type was set "point". "1" means "modify labels", while "2" means "not modify". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
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". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
line_type_lgd |
If plot_type was set "vertical_line" or "horizontal_line", control the appearance of the line type legend in the plotting region. "1" means "show", while "2" means "hide". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
line_type_lgd_name |
Title of the line type legend, when line_type_lgd was set "1", like "linetype". Null value will result in an empty title. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
line_type_lgd_mdy_label |
The labels of legend in linetype legend, when line_type_lgd was set "1" and plot_type was set "vertical_line" or "horizontal_line". "1" means "modify labels", while "2" means "not modify". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
line_type_lgd_label |
If line_type_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". The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
lgd_pos |
The position to place the legend. "1" means "right", while "2" means "bottom". |
lgd_space_size |
Percent of legend size relative to the main plotting region. Applicable values are numbers in [0-1], like 0.04. |
lgd_intra_size |
Intra-spacing between different legends, like 40. |
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". |
ylabel |
Show or hide tick labels on the Y-axis. "1" means "show", while "2" means "hide". |
height_layer |
Height of the track as 0.06. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
margin_layer |
Margin size of the track as 0.01. The number of values received through this parameter should be equal to that of the values received through the data.track parameter. |
chr_plotype |
All chromosomes can either be concatenated or separated. "1" means "Concatenated chromosomes", while "2" means "Separated chromosomes". |
plot_direct |
Chromosomes could be aligned to the horizontal axis or the vertical axis. "1" means "Horizontally aligned", while "2" means "Vertically aligned". |
theme_sty |
Select one figure theme from themes list "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". |
ytitle |
Y axis title, like "Value". |
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". |
Author(s)
Yiming Yu, Wen Yao
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | data.chr <- read.table(system.file("examples/single_genome/genome_data.txt",
package="shinyChromosomeR"), header=TRUE, as.is=TRUE, sep="\t")
head(data.chr)
data.track.file <- c(system.file("examples/single_genome/point.txt", package="shinyChromosomeR"),
system.file("examples/single_genome/line.txt", package="shinyChromosomeR"))
data.track.file
data.track <- lapply(data.track.file, function(x){
dt <- read.table(x, header=TRUE, as.is=TRUE, sep="\t")
return(dt)
})
single_genome_plot(data.chr=data.chr, data.track=data.track, plot_type=c("point", "line"))
|
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