| Type: | Package |
| Title: | Representation Tool For Output Of Connectivity Map (CMap) Analysis |
| Date: | 2019-10-25 |
| Version: | 0.1.0 |
| Author: | Raphaël Bonnet [aut, cre], Jean-François Peyron[aut,ths] |
| Maintainer: | Raphaël Bonnet <raphael.bonnet@univ-cotedazur.fr> |
| Description: | Automatically displays graphical visualization for exported data table (permutated results) from Connectivity Map (CMap) (2006) <doi:10.1126/science.1132939>. It allows the representation of the statistics (p-value and enrichment) according to each cell lines in the form of a bubble plot. |
| BugReports: | https://github.com/Peyronlab/CMapViz/issues |
| Imports: | readxl, ggplot2, dplyr, scales, reshape2, stringr |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 6.1.1 |
| Suggests: | spelling |
| Language: | en-US |
| NeedsCompilation: | no |
| Packaged: | 2019-11-07 10:05:48 UTC; raphael |
| Repository: | CRAN |
| Date/Publication: | 2019-11-07 11:10:13 UTC |
Bubble plot of CMap output table
Description
This function allows the user to represent the Connectivity Map (CMap) result table (broadinstitute) under the form of a bubble plot representing statistics and cell lines: - each drug is represented along the y axis according to its enrichment value - each drug is represented along the x axis according to the cell line tested and within the cell line according to batch specificity (0-50
Usage
bubble_plot(path, plot, enrichment, abs.enrich.cutoff=NULL, n.rep.cutoff=NULL ,
jittering=FALSE, return.gg.table= FALSE, output_path = NULL)
Arguments
path |
path of the excel file (permutated results) |
plot |
what data to plot: molecules only (plot="molecules") or molecules by cell lines batch (plot="cell.lines") |
enrichment |
whether to plot positive or negative enrichment |
abs.enrich.cutoff |
minimum value of enrichment to include a batch |
n.rep.cutoff |
minimum number of replicates to include a batch (default=NULL) |
jittering |
whether apply jittering to the values to avoid points overlap |
return.gg.table |
table prepared for ggplot, allows the user to customize the graphical representation |
output_path |
path for the experiment output folder, returns data table and figure (default=NULL) |
Value
ggplot object - bubble plot
Examples
file.path <- system.file("extdata", "example.xls", package = "CMapViz")
#display results by cell lines, with negative enrichment (absolute cutoff: 0.5), and at least n=5.
#molecule position with respect of dotted line is the specificity of the molecule itself:
#left side of dotted line if specificity < 50 or right side of dotted line if specificity > 50 )
bubble_plot(file.path,
plot = "cell.lines", enrichment = "negative", abs.enrich.cutoff = 0.5,
n.rep.cutoff = 5, output_path = NULL
)