dot_plot: Dot-plot - Pacman-plot function

In FlexDotPlot: Flexible Dot Plot

Dot-plot - Pacman-plot function

Description

Create dotplots to represent two discrete factors (x & y) described by several other factors. Each combination of the two discrete factors (x & y) can be described with : 1 continuous factor (setting shape size), 3 continuous or discrete factors (setting shape type, shape color and text on shape).

Usage

dot_plot(
  data.to.plot,
  size_var = NA,
  col_var = NA,
  text_var = NA,
  shape_var = 16,
  size_legend = "",
  col_legend = "",
  shape_legend = "",
  cols.use = "default",
  text.size = NA,
  text.vjust = 0,
  shape_use = "default",
  shape.scale = 12,
  scale.by = "radius",
  scale.min = NA,
  scale.max = NA,
  plot.legend = TRUE,
  do.return = FALSE,
  x.lab.pos = c("both", "top", "bottom", "none"),
  y.lab.pos = c("left", "right", "both", "none"),
  x.lab.size.factor = 1,
  y.lab.size.factor = 1,
  vertical_coloring = NA,
  horizontal_coloring = NA,
  size.breaks.number = 4,
  color.breaks.number = 5,
  shape.breaks.number = 5,
  size.breaks.values = NA,
  color.breaks.values = NA,
  shape.breaks.values = NA,
  display_max_sizes = TRUE,
  transpose = FALSE,
  dend_x_var = NULL,
  dend_y_var = NULL,
  dist_method = c("euclidean", "maximum", "manhattan", "canberra", "binary",
    "minkowski"),
  hclust_method = c("ward.D", "single", "complete", "average", "mcquitty", "median",
    "centroid", "ward.D2"),
  do.plot = TRUE
)

Arguments

data.to.plot	Input data. Can be a list or a data.frame. If data.frame : Column 1 = x axis (Factor); Col2= y axis (Factor). If list : x and y axis are fixed by row and col names of list elements.
size_var	If numeric : Column/List index which control shape sizes. This column/element has to be numeric. Can also be a column/element name or a vector of the same size than the input dataset. Set to NA if you don't want to control shape size.
col_var	If numeric : Column/List index which control shape colors. Can also be a column/element name or a vector of the same size than the input dataset. Set to NA if you don't want to control shape color.
text_var	If numeric : Column/List index which control text to add on shapes. Can also be a column/element name or a vector of the same size than the input dataset. Set to NA if you don't want to add text.
shape_var	If numeric = Similar to pch : square=15; circle=16; triangle=17. Can also be a column/element name or a vector of the same size than the input dataset.
size_legend	Custom name of shape legend.
col_legend	Custom name of shape color.
shape_legend	Name of the shape legend if shape_var is a vector.
cols.use	1 color or a vector containing multiple colors to color shapes. If coloring is continuous, default colors are taken from a "lightgrey" to "blue" gradient. If coloring is discrete, default colors are taken from the default ggplot2 palette.
text.size	Size of text to display on the shapes.
text.vjust	Vertical justification of text to display on the shapes. Default value = 0, which mean no justification. Recommended value is between -0.5 and 0.5.
shape_use	Shapes to uses (only when shape is controled by a discrete factor). Default shapes : \u25A0 \u25CF \u25C6 \u2BC8 \u2BC7 \u2BC6 \u2BC5 \u25D8 \u25D9 \u2726 \u2605 \u2736 \u2737.
shape.scale	Scale the size of the shapes, similar to cex.
scale.by	Scale the size by size or radius.
scale.min	Set lower limit for scaling, use NA for default values.
scale.max	Set upper limit for scaling, use NA for default values.
plot.legend	Plot the legends ?
do.return	Return ggplot2 object ?
x.lab.pos	Where to display x axis labels. This must be one of "bottom","top","both" or "none".
y.lab.pos	Where to display y axis labels. This must be one of "left","right","both"or "none".
x.lab.size.factor	Factor resizing x-axis labels (default=1)
y.lab.size.factor	Factor resizing y-axis labels (default=1)
vertical_coloring	Which color use to color the plot vertically ? (colors are repeated untill the end of the plot). Setting vertical and horizontal coloring at the same time is not recommended !
horizontal_coloring	Which color use to color the plot horizontally ? (colors are repeated untill the end of the plot). Setting vertical and horizontal coloring at the same time is not recommended !
size.breaks.number	Number of shapes with different size to display in the legend. Not used if size.breaks.values is not NA.
color.breaks.number	Number of labels for the color gradient legend. Not used if color.breaks.values is not NA.
shape.breaks.number	Number of shapes to display in the legend. Used when shape is controled by a continuous factor only. Not used if shape.breaks.values is not NA.
size.breaks.values	Vector containing numerical labels for the size legend.
color.breaks.values	Vector containing numerical labels for continuous color legend.
shape.breaks.values	Vector containing numerical labels for continuous shape legend.
display_max_sizes	Boolean : Display max shape size behind each shape ? (Default=TRUE)
transpose	Reverse x axis and y axis ?
dend_x_var	A vector containing Column/List indexes or Column/List names to compute the x axis dendrogramm.
dend_y_var	A vector containing Column/List indexes or Column/List names to compute the y axis dendrogramm.
dist_method	The distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski".
hclust_method	The agglomeration method to be used. This must be one of "single", "complete", "average", "mcquitty", "ward.D", "ward.D2", "centroid" or "median".
do.plot	Print the plot ? (default=TRUE)

Value

Print the plot (if do.plot=TRUE) and return a list containing input data, executed command, resulting dot plot and computed dendrograms (if do.return=TRUE)

Author(s)

Simon Leonard - [e-mail]

Examples

library(FlexDotPlot)
data(CBMC8K_example_data)
dotplot = dot_plot(data.to.plot=CBMC8K_example_data, size_var="RNA.avg.exp.scaled",
col_var="ADT.avg.exp.scaled", text_var="ADT.pct.exp.sup.cutoff",
shape_var="canonical_marker", shape_use = c("\u25CF","\u2737"),x.lab.pos="bottom",
y.lab.pos="left", cols.use=c("lightgrey","orange","red", "darkred"),
size_legend="RNA", col_legend="ADT", shape_legend="Canonical marker ?",
shape.scale =12, text.size=3, plot.legend = TRUE,
size.breaks.number=4, color.breaks.number=4, shape.breaks.number=5,
dend_x_var=c("RNA.avg.exp.scaled","ADT.avg.exp.scaled"),
dend_y_var=c("RNA.avg.exp.scaled","ADT.avg.exp.scaled"),
dist_method="euclidean",hclust_method="ward.D", do.return = TRUE)

FlexDotPlot documentation built on April 5, 2022, 1:14 a.m.