sp_scatterplot: Generating scatter plot

In Tong-Chen/YSX: For Yishengxin Training

Description

Generating scatter plot

Usage

sp_scatterplot(
  data,
  xvariable = NULL,
  yvariable = NULL,
  label_variable = NULL,
  xvariable_order = NULL,
  yvariable_order = NULL,
  color_variable_order = NULL,
  shape_variable_order = NULL,
  manual_color_vector = NULL,
  log_variables = NULL,
  log_transform = "log2",
  size_variable = NULL,
  geom_text_repel = TRUE,
  shape_variable = NULL,
  color_variable = NULL,
  point_hjust = 0,
  line_size = NULL,
  smooth_method = "no smooth",
  alpha = 1,
  jitter = FALSE,
  jitter_text = F,
  scale_size_min = NULL,
  scale_size_max = NULL,
  coordinate_flip = FALSE,
  legend.position = "right",
  xtics_angle = 0,
  title = NULL,
  x_label = NULL,
  y_label = NULL,
  extra_ggplot2_cmd = NULL,
  label_font_size = 3,
  facet = NULL,
  nrow = NULL,
  ncol = NULL,
  scales = "fixed",
  scale_y_way = NULL,
  ...
)

Arguments

data	Data file or dataframe (with header line, the first column is not the rowname, tab seperated).
xvariable	The variable for x axis. NECESSARY, such X_val (one of column names), both text and number works.
yvariable	The variable for y axis. NECESSARY, such as Y_val (one of column names), both text and number works.
label_variable	Label points with given text. Default no-label, accept a string like Samp`` (one of column names) here to label Samp' column text to points.
xvariable_order	The order for x-axis when xvariables are text. Default alphabetical order, accept a string like c('K562','hESC','GM12878','HUVEC','NHEK','IMR90','HMEC').
yvariable_order	The order for y-axis when yvariables are text. Default alphabetical order, accept a string like c('K562','hESC','GM12878','HUVEC','NHEK','IMR90','HMEC').
color_variable_order	The order for color variable. Default alphabetical order, accept a string like c('K562','hESC','GM12878','HUVEC','NHEK','IMR90','HMEC').
shape_variable_order	The order for shape variable. Default alphabetical order, accept a string like c('K562','hESC','GM12878','HUVEC','NHEK','IMR90','HMEC').
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).
log_variables	Get log-transformed data for given variable. Default NULL, means no log10 transform. Accept a vector like c('color') (one or several of column names) to get (-1) * log10(color).
log_transform	Get log-transformed data for log_variables. Default log2, means log2 transform if log_variabels are not null. Accept log10.
size_variable	The variable for point size. Optional, such as a number or a variable like count (one of column names), normally should be number column.
shape_variable	The variable for point shape. Optional, such as shape (one of column names).
color_variable	The variable for point color. Optional, such as color (one of column names).
line_size	line size. Default NULL. Accept a number.
smooth_method	The smooth method one wants to use, eg. auto, lm, glm, gam, loess, rlm. For observations < 1000 default is 'loess', observations >= 1000 defaults to 'gam'. Default 'no smooth' meaning show the real lines and do not smooth lines. Accept auto, lm, glm, gam, loess, rlm.
alpha	Transparency value for points. Optional, such as a number or a variable indicating one data column, normally should be number column (one of column names).
jitter	Jitter points. Normally used when x and y axis variable is in text format or represents group information to avoid point overlaps. Default FALSE.
jitter_text	Make point labels not overlap. Default FALSE.
scale_size_min	Scale size with minimum value specified
scale_size_max	Scale size with maximum value specified
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.
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.
title	Title of picture. Default empty title.
x_label	Xlab label.
y_label	Ylab label.
extra_ggplot2_cmd	Extra ggplot2 commands (currently unsupported)
label_font_size	Label font size. Default system default. Accept a number.
facet	Wrap plots by given column. This is used to put multiple plot in one picture. Used when melted is FALSE, normally a string set (one of column names) should be suitable for this parameter.
nrow	The number of rows one want when melted is used. Default NULL.
ncol	The number of columns one want when melted is used. Default NULL.
scales	Paramter for scales for facet. Default fixed meaning each inner graph
scale_y_way	The way to scale Y-axis like scale_y_log10, coord_trans(y="log10"), scale_y_continuous(trans="log2"), coord_trans(y="log2").
...	Parametes given to sp_ggplot_layout

Value

A ggplot2 object

Examples

scatter_test_data <- data.frame(Samp = letters[1:6], Color = sample(c("group1", "group2", "group3"),6,replace = TRUE),
X_val = runif(6), Y_val = runif(6), Size = sample(4:20, size = 6),
Shape = sample(c("cluster1","cluster2"),6,replace = TRUE))

sp_scatterplot(data=scatter_test_data,xvariable = "X_val",yvariable = "Y_val",
color_variable = "Color", shape_variable= "Shape",
size_variable = "Size",label="Samp",Jitter = TRUE)



## Not run:
scatter_data = "scatter.txt"
sp_scatterplot(data="scatter.txt",xvariable = "X_val",yvariable = "Y_val",
color_variable = "Color", shape_variable= "Shape",size_variable = "Size",
label="Samp", xvariable_order = c(1,3,2), yvariable_order = c(2,1,3),
color_variable_order = c("grp2","grp1","grp3"),
shape_variable_order = c("cluster2","cluster1"),label_font_size=2)

sp_scatterplot(data="scatter.txt",xvariable = "X_val",yvariable = "Y_val", color_variable = "Color", shape_variable= "Shape",
size_variable = "Size",label="Samp",Jitter = TRUE)

sp_scatterplot(data="scatter.txt",xvariable = "X_val",yvariable = "Y_val", color_variable = "Color", shape_variable= "Shape",
size_variable = "Size",label="Samp",Jitter = TRUE,facet = "Color", scales = "free_y")
## End(Not run)

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