sp_barplot: Generating bar plot

In Tong-Chen/YSX: For Yishengxin Training

Description

Generating bar plot

Usage

sp_barplot(
  data,
  color_variable = NULL,
  yvariable = NULL,
  xvariable = NULL,
  melted = TRUE,
  title = NULL,
  x_label = NULL,
  y_label = NULL,
  color_variable_order = NULL,
  xvariable_order = NULL,
  y_add = 0,
  group_variable = NULL,
  add_bar_link = FALSE,
  add_point = F,
  yaxis_scale_mode = NULL,
  facet_variable = NULL,
  stat = "identity",
  bar_mode = "stack",
  facet_variable_order = NULL,
  facet_nrow = NULL,
  facet_ncol = NULL,
  error_bar_variable = NULL,
  base_font_size = 11,
  legend.position = "right",
  xtics = TRUE,
  xtics_angle = 0,
  statistics = FALSE,
  ytics = TRUE,
  manual_color_vector = "Set2",
  facet_scales = "fixed",
  extra_ggplot2_cmd = NULL,
  coordinate_flip = FALSE,
  add_text = FALSE,
  font_path = NULL,
  debug = FALSE,
  filename = NULL,
  ...
)

Arguments

data	Data frame or data file (with header line, the first column will not be treated as row names, tab separated).
color_variable	Name for specifying bars colors (one of column names, should be specified when inputting long format matrix).
yvariable	Name for value column (one of column names, should be specified when inputting long format matrix).
xvariable	Name for x-axis variable (one of column names, should be specified when inputting long format matrix).
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.
title	Title of picture.
x_label	Xlab label.
y_label	Ylab label.
color_variable_order	Set orders of color variable (this can also used to extract specific rows).
xvariable_order	Levels for x-axis variable, suitable when x-axis is not used as a number.
y_add	A number to add if log scale is used. Default 0 meaning the minimum non-zero value would be used.
group_variable	Specify group info for for computing means and SDs.
add_point	Set to TRUE to add each point (specially used when displaying mean values)
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.
facet_variable	Wrap plots by given column (one of column names should be specified). This is used to put multiple plot in one picture.
stat	The ways to show the height of bars. The height of bars represent the numerical values in each group by default (normally in yvariable column of melted data). One can also give count to let the program count the number of items in each group (Normally the color_variable column is used to group 'xvariable' column after melt). Or one can give weight which will sum values of each group. Default identity, accept count when categorical data are given.
bar_mode	The ways to place multiple bars for one group. Multiple bars in same place will be stacked together by default. Giving fill to get stacked percent bar-plot. Giving dodge to arrange multiple bars side-by-side. Default stack, accept dodge, fill.
facet_variable_order	The levels of wrapping to set the order of each group.
facet_nrow	The number of rows one want when facet is used. Default NULL.
facet_ncol	The number of columns one want when facet is used. Default NULL.
error_bar_variable	Error-bar column (one of column names). Specify the column containing error bars.
base_font_size	Font-size. Default 11.
legend.position	Position of legend, accept top, bottom, left, right, none or c(0.8,0.8).
xtics	Display xtics. Default TRUE.
xtics_angle	Rotation angle for a-axis. Default 0.
ytics	Display ytics. Default FALSE.
manual_color_vector	Manually set colors for each geom. Default NULL, meaning using ggplot2 default. Colors like c('red', 'blue', '#6181BD') (number of colors not matter) or a RColorBrewer color set like "BrBG" "PiYG" "PRGn" "PuOr" "RdBu" "RdGy" "RdYlBu" "RdYlGn" "Spectral" "Accent" "Dark2" "Paired" "Pastel1" "Pastel2" "Set1" "Set2" "Set3" "Blues" "BuGn" "BuPu" "GnBu" "Greens" "Greys" "Oranges" "OrRd" "PuBu" "PuBuGn" "PuRd" "Purples" "RdPu" "Reds" "YlGn" "YlGnBu" "YlOrBr" "YlOrRd" (check http://www.sthda.com/english/wiki/colors-in-r for more).
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).
extra_ggplot2_cmd	Other legal R codes for ggplot2 will be given here.
coordinate_flip	Flip cartesian coordinates so that horizontal becomes vertical, and vertical, horizontal. This is primarily useful for converting geoms and statistics which display y conditional on x, to x conditional on y.
add_text	Add text to bar. Default FALSE.
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.
filename	Output picture to given file.
...

Value

A ggplot2 object

Examples

bar_test_data <- data.frame(ID = letters[1:4], Gene = letters[c(8,8,9,9,10,10,11,11)], Expr = runif(16))
sp_barplot(data = bar_test_data, xvariable = "ID", yvariable = "Expr", color_variable = "Gene")

## Not run:
bar_data = "bar.data"

sp_barplot(data = bar_data, xvariable = "ID", yvariable = "Expr", color_variable = "Gene")
## End(Not run)

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