gess_res_vis: GESS Result Visualization

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

GESS Result Visualization

Description

The function allows to summarize the ranking scores of selected perturbagens for GESS results across cell types along with cell type classifications, such as normal and tumor cells. In the resulting plot the perturbagens are drugs (along x-axis) and the ranking scores are LINCS' NCS values (y-axis). For each drug the NCS values are plotted for each cell type as differently colored dots, while their shape indicates the cell type class.

Usage

gess_res_vis(gess_tb, drugs, col, cell_group = "all", ...)

Arguments

gess_tb	tibble in the 'result' slot of the gessResult object, can be extracted via result accessor function
drugs	character vector of selected drugs
col	character(1), name of the score column in 'gess_tb', e.g., "NCS" if the result table is from LINCS method. Can also be set as "rank", this way it will show the ranks of each drug in different cell types.
cell_group	character(1), one of "all", "normal", or "tumor". If "all", it will show scores of each drug in both tumor and normal cell types. If "normal" or "tumor", it will only show normal or tumor cell types.
...	Other arguments passed on to geom_point

Value

plot visualizing GESS results

References

Subramanian, A., Narayan, R., Corsello, S. M., Peck, D. D., Natoli, T. E., Lu, X., Golub, T. R. (2017). A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. Cell, 171 (6), 1437-1452.e17. URL: https://doi.org/10.1016/j.cell.2017.10.049

Examples

gr <- gessResult(result=dplyr::tibble(pert=c("p1", "p1", "p2", "p3"),
                                      cell=c("MCF7", "SKB", "MCF7", "SKB"),
                                      type=rep("trt_cp", 4),
                                      NCS=c(1.2, 1, 0.9, 0.6)),
                 query=list(up="a", down="b"), 
                 gess_method="LINCS", refdb="path/to/refdb")
gess_res_vis(result(gr), drugs=c("p1","p2"), col="NCS")

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.