library(ggcyto) dataDir <- system.file("extdata",package="flowWorkspaceData") gs <- load_gs(list.files(dataDir, pattern = "gs_bcell_auto",full = TRUE)) data(GvHD) fs <- GvHD[subset(pData(GvHD), Patient %in%5 & Visit %in% c(5:6))[["name"]]]
flowSet
geom_density layer is used for one-dimensional plot.
autoplot(fs, x = 'FSC-H')
geom_hex layer is added for 2d plot.
autoplot(fs, x = 'FSC-H', y = 'SSC-H', bins = 64)
## flowFrame For the flowFrame, it can display one-dimensional plots for all channels by not supplying the x argument.
GatingSet
autoplot(gs, "CD3", bins = 64)
Here are some default settings applied:
- The instrument range is applied by default (through
ggcyto_par_set(limits = "instrument")). - “CD3” gate is plotted aganst its the parent population: “Live”."
- Axis labels are inverse transformed through
axis_x_inverse_trans/axis_x_inverse_trans.
Multiple gates that share the same parent can be plotted together.
GatingHierarchy
Multiple cell populations with their asssociated gates can be plotted in different panels of the same plot.
gh <- gs[[1]] nodes <- gs_get_pop_paths(gh, path = "auto")[c(3:6)] nodes
## [1] "lymph" "Live" "CD20" "CD19"autoplot(gh, nodes, bins = 64)
ggcyto_arrange
Optionally we can manually arrange it as a gtable object and manipulate the layout afterwards.
# get ggcyto_GatingLayout object from first sample res <- autoplot(gs[[1]], nodes, bins = 64) class(res)
## [1] "ggcyto_GatingLayout"
## attr(,"package")
## [1] "ggcyto"# arrange it as one-row gtable object gt <- ggcyto_arrange(res, nrow = 1) gt
## TableGrob (2 x 4) "arrange": 5 grobs
## z cells name grob
## lymph 1 (2-2,1-1) arrange gtable[layout]
## Live 2 (2-2,2-2) arrange gtable[layout]
## CD20 3 (2-2,3-3) arrange gtable[layout]
## CD19 4 (2-2,4-4) arrange gtable[layout]
## 5 (1-1,1-4) arrange text[GRID.text.1425]# do the same to the second sample gt2 <- ggcyto_arrange(autoplot(gs[[2]], nodes, bins = 64), nrow = 1) # combine the two and print it on the sampe page gt3 <- gridExtra::gtable_rbind(gt, gt2) plot(gt3)
