SIDAP

An Integrated Mass Cytometry Data Analysis Pipeline

This is a BETA release of SIDAP, Analyse the CYTOF data by simultaneous illustration of diversity and progression. To use this package, you will need the R statistical computing environment (R (>= 2.7.0)) and several dependent packages (tcltk, flowCore, mclust, gplots, igraph, reshape, graphics, ggplot2, e1071, lle, vegan) available through Bioconductor.

sidap_0.99.9

SIDAP package was accepted by bioconductor, new version sidap_0.99.9 was uploaded for release on bioconductor. SIDAP devel-version URL. You can download the package tarball or compiled file, install it locally. But you need to install the dependent packages manually. In order to use the devel version of Bioconductor (Bioconductor 3.1), you must install R-devel, available from:

Source ftp://ftp.stat.math.ethz.ch/Software/R/
Mac http://r.research.att.com/
Windows http://cran.r-project.org/bin/windows/base/rdevel.html

Then, in R-devel, do the following:

    source("http://bioconductor.org/biocLite.R")
    ##Install the package
    biocLite("sidap")

Package Updates:

a new vignette was added to the package, SIDAP: run with an example. Explaining how to use the package with a demo
functions are split into smaller ones, help page with runnable examples are added
a package help page was added to help users get oriented right away. and user can link to other functions from this page
modified the marker matching function, change perl matching method for exact matching, no fuzz match
added scaleMethod option for the heatmap plotting

sidap_0.99.6

package updates:
- adjusted graph to fit for multiple samples (auto adjust)
- adjusted the shape(sample) and colour(cluster) palette for sample size bigger than 4 and clusters more than 10
- adjusted the heatmap plot(legend, label, title) to auto fit for saving into PDF
- auto check and report the odd markers which are not shown in the FCS files
- added the vignette (SIDAP analysis workflow)
- fixed several minor bugs in GUI

package installation

2.1 Download this package to your local directory, then start the R session, and change the working directory to where the sidap_0.99.6.tar.gz is. Since this package has not been submitted to any public archive, you need to check if you have installed all the dependent packages listed above. For this checking, you can download the sidap_firstRun.R function for auto checking and installation.

## copy these codes to the console to install the dependent packages 
sidap_firstRun <- function() {
    if (!require(tcltk, quietly = TRUE)) {
        install.packages("tcltk") 
    }
    if (!require(Rtsne, quietly = TRUE)) {
        install.packages("Rtsne")
    }
    if (!require(flowCore)) {
        source("http://bioconductor.org/biocLite.R")
        biocLite("flowCore", ask = FALSE)
    }
    if (!require(mclust)) {
        source("http://bioconductor.org/biocLite.R")
        biocLite("mclust", ask = FALSE)
    }
    if (!require(gplots)) {
        source("http://bioconductor.org/biocLite.R")
        biocLite("gplots", ask = FALSE)
    }
    if (!require(reshape)) {
        source("http://bioconductor.org/biocLite.R")
        biocLite("reshape", ask = FALSE)
    }
    if (!require(graphics)) {
        source("http://bioconductor.org/biocLite.R")
        biocLite("graphics", ask = FALSE)
    }
    if (!require(ggplot2)) {
        source("http://bioconductor.org/biocLite.R")
        biocLite("ggplot2", ask = FALSE)
    }
    if (!require(e1071)) {
        source("http://bioconductor.org/biocLite.R")
        biocLite("e1071", ask = FALSE)
    }
    if (!require(lle)) {
        source("http://bioconductor.org/biocLite.R")
        biocLite("lle", ask = FALSE)
    }
    if (!require(vegan)) {
        source("http://bioconductor.org/biocLite.R")
        biocLite("vegan", ask = FALSE)
    }
}

sidap_firstRun()

then install the package with following commands:

install.packages("sidap_0.99.6.tar.gz", repos = NULL, type = "source")

2.2 browse the vignette
```
browseVignettes(package = "sidap")
```
2.3 Running the workhorse function cytof_tsne_densvm
```
library(sidap)
?cytof_tsne_densvm   # read the help page for this function
cytof_tsne_densvm()  # input your parameters
```
Otherwise, if you are not comfortable with command, sidap provides a user friendly GUI for the workhorse function cytof_tsne_densvm in this package.
```
library(sidap)
cytof_tsne_densvm_GUI()
```
Check the vignettee and help pages for more information about this package and the using of the workhorse function.

sidap_0.99.5

package updates:
- added the prefix(baseName) to all output files
- reorganize the codes for easier maintenance
- added Roxygen documentation to the export functions
- removed inside package attach, like library() or require()
- organized the dependent packages to the NAMESPACE
- added the cluster plot for whole fcs data and grid cluster plot for each fcs file
- fixed several minor bugs
package installation
- 2.1 Download this package to your local directory, then start the R session, and change the working directory to where the sidap_0.99.5.tar.gz is. Since this package has not been submitted to any public archive, you need to check if you have installed all the dependent packages listed above. For this checking, you can download the sidap_firstRun.R function for auto checking and installation.
```
source(sidap_firstRun.R)
sidap_firstRun()
```
  then install the package with following commands:
```
install.packages("sidap_0.99.5.tar.gz", repos = NULL, type = "source")
```
- 2.2 check the notes in sidap_0.99.4 for package running

sidap_0.99.4

1.Download this package to your local directory, then start the R session, and change the working directory to where the "sidap_0.99.3.tar.gz" is, then type the following commands:

install.packages("sidap_0.99.4.tar.gz", repos = NULL, type = "source")

2.Running this package is depended on several other R packages(listed above) which available through Bioconductor. Running the workhorse function cytof_tsne_densvm will firstly help check if the dependent packages are available, and will ask for user's permission before installing these dependent packages.

library(sidap)
?cytof_tsne_densvm   # read the help page for this function
cytof_tsne_densvm()  # input your parameters

Otherwise, if you are not comfortable with command, sidap provides a user friendly GUI for the workhorse function cytof_tsne_densvm in this package.

library(sidap)
cytof_tsne_densvm_GUI()

3.Check the help pages for more information about this package and the using of the workhorse function.

NOTE: This package is in the BETA stage of development, it has been password protected awaiting publication, but will be released as soon as published. New features will continue to be added, please take note for changes in this package. This BETA version is tested on Windows and Mac OS. Using the GUI version of the workhorse function on Mac OS, please check to see whether the X11 windowing system (X Windows) has already been installed on your computer. For OS X 10.6 and 10.7, the file X11.app should appear in the Utilities folder under Applications in the finder. This application should always be installed under OS X 10.7. For OS X 10.8 or 10.9, the file is named XQuartz.app and is no longer included with the operating system, you need to install XQuartz yourself. Install XQuartz from http://xquartz.macosforge.org.

Download the disk image (dmg) file for XQuartz.
When you open this file by double-clicking on it, you'll find XQuartz.pkg, double-click on it to run the installer, clicking through all the defaults.
After the installer runs, you'll have to log out and back on to your Mac OS X account.