cytofkit: cytofkit: an integrated mass cytometry data analysis pipeline

In cytofkit: cytofkit: an integrated mass cytometry data analysis pipeline

Description

The main function to drive the cytofkit workflow.

Usage

cytofkit(fcsFiles = getwd(), markers = "parameter.txt",
  projectName = "cytofkit", ifCompensation = FALSE,
  transformMethod = c("autoLgcl", "cytofAsinh", "logicle", "arcsinh", "none"),
  mergeMethod = c("ceil", "all", "min", "fixed"), fixedNum = 10000,
  dimReductionMethod = c("tsne", "pca", "isomap"),
  clusterMethods = c("Rphenograph", "ClusterX", "DensVM", "FlowSOM", "NULL"),
  visualizationMethods = c("tsne", "pca", "isomap", "NULL"),
  progressionMethod = c("NULL", "diffusionmap", "isomap"),
  Rphenograph_k = 30, FlowSOM_k = 40, seed = NULL,
  clusterSampleSize = 500, resultDir = getwd(), saveResults = TRUE,
  saveObject = TRUE, openShinyAPP = FALSE, ...)

Arguments

fcsFiles	It can be either the path where your FCS files are stored or a vector of FCS file names.
markers	It can be either a text file that containing markers to be used for analysis or a vector of the marker names.
projectName	A prefix that will be added to the names of all result files.
ifCompensation	Boolean value, to apply compensation contained in FCS, or a compensation matrix.
transformMethod	Data Transformation method, including autoLgcl, cytofAsinh, logicle and arcsinh, or none to avoid transformation.
mergeMethod	When multiple fcs files are selected, cells can be combined using one of the four different methods including ceil, all, min, fixed. The default option is ceil, up to a fixed number (specified by fixedNum) of cells are sampled without replacement from each fcs file and combined for analysis. all: all cells from each fcs file are combined for analysis. min: The minimum number of cells among all the selected fcs files are sampled from each fcs file and combined for analysis. fixed: a fixed num (specified by fixedNum) of cells are sampled (with replacement when the total number of cell is less than fixedNum) from each fcs file and combined for analysis.
fixedNum	The fixed number of cells to be extracted from each FCS file.
dimReductionMethod	The method used for dimensionality reduction, including tsne, pca and isomap.
clusterMethods	The clustering method(s) used for subpopulation detection, including DensVM, ClusterX, Rphenograph and FlowSOM. Multiple selections are accepted.
visualizationMethods	The method(s) used for visualize the cluster data, including tsne, pca and isomap. Multiple selections are accepted.
progressionMethod	Use the first ordination score of isomap to estimated the progression order of cells, choose NULL to ignore.
Rphenograph_k	Integer number of nearest neighbours to pass to Rphenograph.
FlowSOM_k	Number of clusters for meta clustering in FlowSOM.
seed	Integer to set a seed for reproducible results.
clusterSampleSize	The uniform size of each cluster.
resultDir	The directory where result files will be generated.
saveResults	Save the results, and the post-processing results including scatter plot, heatmap, and statistical results.
saveObject	Save the results into RData objects for loading back to R for further analysis
openShinyAPP	Opens the shinyAPP automatically when the analysis was done, default FALSE.
...	Other arguments passed to cytof_exprsExtract

Details

cytofkit works as the main funciton to perform the analysis of one or multiple FCS files. The workflow contains data merging from multiple FCS file, expression data transformation, dimensionality reduction with PCA, isomap or tsne (default), clustering analysis with methods includes DensVM, ClusterX, Rphenograph) and FlowSOM for subpopulation detection, and estimation of cellular progression using isomap. The analysis results can be visualized using scatter plot, heatmap plot or progression plot. Dimension reduced data and cluster labels will be saved back to new copies of FCS files. By default the analysis results will be automatically saved under resultDir for further annotation. Moreover An interactive web application is provided for interactive exploration of the analysis results, see cytofkitShinyAPP.

Value

a list containing expressionData, dimReductionMethod, visualizationMethods, dimReducedRes, clusterRes, progressionRes, projectName, rawFCSdir and resultDir. If choose 'saveResults = TRUE', results will be saved into files under resultDir.

Author(s)

Hao Chen, Jinmiao Chen

References

https://github.com/JinmiaoChenLab/cytofkit

See Also

cytofkit, cytofkit_GUI, cytofkitShinyAPP

Examples

dir <- system.file('extdata',package='cytofkit')
file <- list.files(dir, pattern='.fcs$', full=TRUE)
parameters <- list.files(dir, pattern='.txt$', full=TRUE)
## remove the hash symbol to run the following command
#cytofkit(fcsFile = file, markers = parameters) 

Example output

Loading required package: ggplot2
Loading required package: plyr
Warning message:
no DISPLAY variable so Tk is not available 

cytofkit documentation built on Nov. 1, 2018, 3:50 a.m.