psiplot v2.3.0

This release contains many new features and bug fixes.

Subgrouping and multi-event plots (from @jtapial #7)

• Support for sample subgroups in all plot functions, through the config files. PSIs of samples in a subgroup are averaged and displayed as a single data point. Confidence intervals are computed by fitting a joint beta distribution to a population of points sampled from beta distributions coming from the individual samples, and then applying the same method as for single samples.
• Support for plotting multiple events in the same PSI plot, with events identified with different colours, and samples identified by the color background.
• Support for sample columns containing suffixes (e.g. "Sample1-cRPKM", while the config says only "Sample1").
• Support for gene expression tables containing both cRPKM and raw read counts (similar to the PSI and QC columns for events).
• Big changes in the preprocess_sample_colors function and its output, to allow for all this.
• Use of dplyr (and tidyverse in general) instead of plyr.
• README contents moved to vignette

Simplified requirements for configuration file (#8)

• The columns Order and RColorCode in the configuration file are now optional. Only columns SampleName and GroupName are mandatory. This should simplify the minimum requirements needed to create a functional config.
  • Without Order, the order defaults to 1,2,...,N where 1 is the first row of the config
    and N is the last row.
  • Without RColorCode, the default ggplot2 color palette is used.

psiplot v2.1.1

Some bug fixes for plot_expr()

psiplot v2.1.0

This release contains new features and some internal updates. In addition, this release now requires R version 3.1 or higher and ggplot2 version 2.0 or higher.

Installation

Option 1

Install this release using devtools:

devtools::install_github("kcha/psiplot", ref = "v2.1.0")

Option 2

Download the compressed tar archive (or zip) and start R in the directory where it was saved. Then issue the command:

install.packages("psiplot-2.1.0.tar.gz", type = "source", repos = NULL)

Change log

• Replace show_guides with show.legend to match API of ggplot2 version 2.*.
• Update README
• plot_multi has been further developed:
  • Use heatmap.2 from gplots package to produce heatmap. To minimize dependencies, this package is optional and needs to be manually installed (install.packages("gplots")). In the absence of gplots, ggplot2 will be used as before.
  • Events and samples can be clustered using options cluster_rows and cluster_cols, respectively.
  • Add fill option for providing custom colours
  • Simply format of row names
  • See ?plot_multi for full set of options
• Retire warning for deprecated lines option
• The option plot in plot_event and plot_expr is deprecated (will issue warning if used).
• Other documentation updates

psiplot v2.0.1

This release contains minor updates.

• plot_event: update default ylim set to (0,100) from (1,100).

psiplot v2.0.0

Version 2.0.0 now uses ggplot2 to generate plots in plot_event and plot_expr. In addition to outputting a plot, a ggplot2 object is returned.

• Printing of the plot can be suppressed with plot = FALSE.
• The option lines in plot_event and plot_expr is deprecated (will issue warning if used).
• Imports plyr for calculating group means.

NEW

• plot_multi: a new experimental function that will generate a heatmap of PSI values for two or more events:

plot_multi(psi)

Installation

Download the compressed tar archive (or zip) and start R in the directory where it was saved. Then issue the command:

install.packages("psiplot-2.0.0.tar.gz", type = "source", repos = NULL)

psiplot v1.1.2

• Change y-axis labels to be horizontal (e.g. las = 1)

psiplot v1.1.1

• Changed minimum of y-axis to start at 0 for plot_expr() (#2)
• Added check if config and input data does has 0 matching samples (#3)
• Other minor updates to documentation

psiplot v1.1.0

New features and updates

• plot_expr: psiplot can now plot cRPKMs. For example, using the new sample dataset crpkm:

plot_expr(crpkm[1,], config = config)

• Renamed sample datasets to: psi and config (#1)
• Deprecated xlim argument in plot_event - it shouldn't really be used

psiplot v1.0

This is the first release of psiplot in the form of an R package.

Report bugs in https://github.com/kcha/psiplot/issues.

Installation

Download the compressed tar archive and start R in the directory where it was saved. Then issue the command:

install.packages("v1.0.tar.gz", type = "source", repos = NULL)