sp_histogram: Generating histogram plot

In Tong-Chen/YSX: For Yishengxin Training

Description

Generating histogram plot

Usage

sp_histogram(
  data,
  melted = FALSE,
  xvariable = NULL,
  color_variable = NULL,
  color_variable_order = NULL,
  group_variable = NULL,
  group_variable_order = NULL,
  value_scale = 1,
  facet_variable = NULL,
  facet_variable_order = NULL,
  maximum_allowed = Inf,
  yaxis_statistics = "count/sum(count)",
  plot_type = "line",
  binwidth = NULL,
  hist_bar_position = "identity",
  alpha = 0.4,
  yaxis_scale_mode = NULL,
  y_add = 0,
  fill_area = FALSE,
  line_size = 1,
  add_mean_value_vline = FALSE,
  manual_color_vector = "Accent",
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  xtics = TRUE,
  ytics = TRUE,
  legend.position = "right",
  xtics_angle = 0,
  manual_xtics_value = NULL,
  manual_xtics_pos = NULL,
  custom_vline_x_position = NULL,
  custom_vline_anno = NULL,
  x_label = NULL,
  y_label = NULL,
  title = "",
  font_path = NULL,
  debug = F,
  extra_ggplot2_cmd = NULL,
  filename = NULL,
  base_font_size = 11,
  ...
)

Arguments

data	Data frame or data file (with header line, the first column will not be treated as the row-names, tab separated)
melted	TRUE for dealing with long format matrix, the program will skip melt preprocess. If input is wide format matrix, this parameter should be set to FALSE.
xvariable	Specify the column name used as Y-axis value (one of column names, should be specified when inputting long format matrix).
color_variable	Specify the column name used as color variable.
color_variable_order	Levels for color variable to set their appearing order. Accept a vector like c('ctcf','h3k27ac') (normally whole or a subset of unique values of one column with order specified).
group_variable	Specify the column name used as group variable.
group_variable_order	Levels for color variable to set their appearing order. Accept a vector like c('ctcf','h3k27ac') (normally whole or a subset of unique values of one column with order specified).
value_scale	Scale value. All values will be divided by supplied one. Default 1.
facet_variable	Wrap plots by given column (one of column names should be specified). This is used to put multiple plot in one picture.
facet_variable_order	Order of facets (to set the appearance order of each subplot). Accept a vector like c('ctcf','h3k27ac') (normally whole or a subset of unique values of one column with order specified).
maximum_allowed	The largest value allowed. Values other than this will be set as this value. Default Inf.
yaxis_statistics	Plot with density or count or frequency in y-axis. Default frequency, accept density, count. When plot_type is both, 'frequency“ will be given here.
plot_type	Plot frequency or density or hist or both frequency and histogram. Default line means frequency accept density_line, hist or both.
binwidth	The value for binwidth`` (like the width of each bin) in geom_density, and binwidthforgeom_histogram'.
hist_bar_position	Position parameter for hist bars. Default identity, accept dodge.
yaxis_scale_mode	Give the following scale_y_log10(), coord_trans(y="log10"), or other legal command for ggplot2 or simply log2 to set the scale way.
y_add	A number to add if log scale is used. Default 0 meaning the minimum non-zero value would be used.
fill_area	Fill the area if TRUE. Default FALSE.
line_size	line size. Default 1. Accept a number.
add_mean_value_vline	Add mean value as vline. Default FALSE, accept TRUE.
facet_scales	Paramter for scales for facet. Default fixed meaning each inner graph use same scale (x,y range), free (variable x, y ranges for each sub-plot), free_x (variable x ranges for each sub-plot), free_y (variable y ranges for each sub-plot).
facet_ncol	The number of columns one want when facet is used. Default NULL.
facet_nrow	The number of rows one want when facet is used. Default NULL.
xtics	Show the X axis.
ytics	Show the Y axis.
legend.position	Position of legend, accept top, bottom, left, right, none or c(0.8,0.8).
xtics_angle	Rotation angle for a-axis. Default 0.
manual_xtics_value	Manually set the values of xtics when manual_xtics_position is specified. Default the content of manual_xtics_position when manual_xtics_position is specified, accept a series of numbers in following format "c(1,2,3,4,5)" or other R code that can generate a vector to set the value of manual xtics.
manual_xtics_pos	Manually set the positions of xtics. Default FALSE, accept a series of numbers in following format "c(1,2,3,4,5)" or other R code that can generate a vector to set the position of manual xtics.
custom_vline_x_position	A vector of coordinates for vertical lines.
custom_vline_anno	Annotation text for each vertical line.
x_label	Xlab label.
y_label	Ylab label.
title	Title of picture.
font_path	Specify font type. Give a path for one font type file like '/etc/fonts/Arial.ttf' or 'HeiArial.ttc'(if in current directory), Default system default.
extra_ggplot2_cmd	Extra ggplot2 commands (currently unsupported)
filename	Output picture to given file.
...	Other parameters given to sp_ggplot_layout

Value

A ggplot2 object

Examples

histogram_test_data <- data.frame(Type = letters[1:2], Value = runif(80))
sp_histogram(data = histogram_test_data, xvariable = "Value", color_variable = "Type",
 plot_type = "both", yaxis_statistics = "count/sum(count)")

## Not run:
input <- "histogram.data"
sp_histogram(data=input, xvariable = "Value", color_variable = "Type",
 plot_type = "both", yaxis_statistics = "count/sum(count)")
## End(Not run)

Tong-Chen/YSX documentation built on Jan. 25, 2021, 2:49 a.m.