plot.seqData {pmartR}

Plot seqData Object

Description

For plotting seqData S3 objects

Usage

## S3 method for class 'seqData'
plot(
  x,
  order_by = NULL,
  color_by = NULL,
  facet_by = NULL,
  facet_cols = NULL,
  interactive = FALSE,
  x_lab = NULL,
  y_lab = NULL,
  x_lab_size = 11,
  y_lab_size = 11,
  x_lab_angle = 90,
  title_lab = NULL,
  title_lab_size = 14,
  legend_lab = NULL,
  legend_position = "right",
  ylimit = NULL,
  bw_theme = TRUE,
  palette = NULL,
  use_VizSampNames = FALSE,
  transformation = NULL,
  ...
)

Arguments

x

seqData object

order_by

character string specifying the column name of f_data by which to order the boxplots. If order_by is "Group", the boxplots will be ordered by the group variable from the group_designation function. If NULL (default), the boxplots will be displayed in the order they appear in the data.

color_by

character string specifying the column name of f_data by which to color the boxplots. If color_by is "Group", the boxplots will be colored by the group variable from the group_designation function. If NULL (default), the boxplots will have one default color.

facet_by

character string specifying the column name of f_data with which to create a facet plot. Default value is NULL.

facet_cols

optional integer specifying the number of columns to show in the facet plot.

interactive

logical value. If TRUE produces an interactive plot.

x_lab

character string specifying the x-axis label.

y_lab

character string specifying the y-axis label. The default is NULL in which case the y-axis label will be the metric selected for the metric argument.

x_lab_size

integer value indicating the font size for the x-axis. The default is 11.

y_lab_size

integer value indicating the font size for the y-axis. The default is 11.

x_lab_angle

integer value indicating the angle of x-axis labels. The default is 0.

title_lab

character string specifying the plot title.

title_lab_size

integer value indicating the font size of the plot title. The default is 14.

legend_lab

character string specifying the legend title.

legend_position

character string specifying the position of the legend. Can be one of "right", "left", "top", "bottom", or "none". The default is "none".

ylimit

numeric vector of length 2 specifying y-axis lower and upper limits.

bw_theme

logical value. If TRUE uses the ggplot2 black and white theme.

palette

character string indicating the name of the RColorBrewer palette to use. For a list of available options see the details section in RColorBrewer.

use_VizSampNames

logical value. Indicates whether to use custom sample names. The default is FALSE.

transformation

character string. String of length 1 defining a transformation for visualizing count data. Valid options are 'lcpm', 'upper', and 'median'. 'lcpm' - For each column: scale column intensities by (total column sum/1 million), then log2 transform. 'median' - For each column: scale column intensities by median column intensities, then back-transform to original scale. 'upper' - For each column: scale column intensities by 75th quantile column intensities, then back-transform to original scale. For 'median' and 'upper' options, all zeros are converted to NAs.

...

further arguments passed to or from other methods.

Value

ggplot2 plot object if interactive is FALSE, or plotly plot object if interactive is TRUE

Examples

library(pmartRdata)
plot(rnaseq_object, transformation = "lcpm")