knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
# Load required packages library(CytoExploreR) # Setup Activation samples gs <- cyto_setup("Activation-Samples", gatingTemplate = "Manual-Gating.csv") # Apply compensation gs <- cyto_compensate(gs) # Transform fluorescent channels trans <- cyto_transformer_logicle(gs) gs <- cyto_transform(gs, trans = trans) # Extract root cytoset cs <- cyto_extract(gs, "root")
cyto_gate_draw(cs, alias = "Cells", channels = c("FSC-A","SSC-A"), type = "boundary")
knitr::include_graphics('Gating/Manual-Gating-1.gif')
cyto_gate_draw(cs, alias = "Cells", channels = "FSC-A", type = "boundary")
knitr::include_graphics('Gating/Manual-Gating-2.gif')
# Rectangle gate cyto_gate_draw(cs, alias = "CD4 T Cells", channels = c("CD4", "CD8"), type = "rectangle", axes_trans = trans)
knitr::include_graphics('Gating/Manual-Gating-3.gif')
# Polygon gate cyto_gate_draw(cs, alias = "Cells", channels = c("FSC-A", "SSC-A"), type = "polygon")
knitr::include_graphics('Gating/Manual-Gating-4.gif')
# Ellipse gate cyto_gate_draw(cs, alias = "CD8 T Cells", channels = c("CD4", "CD8"), type = "ellipse", axes_trans = trans)
knitr::include_graphics('Gating/Manual-Gating-5.gif')
# Interval gate cyto_gate_draw(cs, alias = "T Cells", channels = c("Va2", "CD44"), type = "interval", axes_trans = trans)
knitr::include_graphics('Gating/Manual-Gating-6.gif')
# Interval gate cyto_gate_draw(cs, alias = "T Cells", channels = "Va2", type = "interval", axes_trans = trans)
knitr::include_graphics('Gating/Manual-Gating-7.gif')
# Threshold gate cyto_gate_draw(cs, alias = "Dead Cells", channels = c("Hoechst-405", "Hoechst-430"), type = "threshold", axes_trans = trans)
knitr::include_graphics('Gating/Manual-Gating-8.gif')
# Threshold gate cyto_gate_draw(cs, alias = "T Cells", channels = "Va2", type = "threshold", axes_trans = trans)
knitr::include_graphics('Gating/Manual-Gating-9.gif')
# Quadrant gate cyto_gate_draw(cs, alias = c("A","B","C","D"), channels = c("CD4","CD8"), type = "quadrant", axes_trans = trans)
knitr::include_graphics('Gating/Manual-Gating-10.gif')
# Web gate cyto_gate_draw(cs, alias = c("A","B","C","D"), channels = c("CD4","CD8"), type = "web", axes_trans = trans)
knitr::include_graphics('Gating/Manual-Gating-11.gif')
# Multiple gates cyto_gate_draw(cs, alias = c("CD4","CD8"), channels = c("CD4","CD8"), type = "rectangle", axes_trans = trans)
knitr::include_graphics('Gating/Manual-Gating-12.gif')
# Multiple gates cyto_gate_draw(cs, alias = c("CD4","CD8"), channels = c("CD4","CD8"), type = c("rectangle", "ellipse"), axes_trans = trans)
knitr::include_graphics('Gating/Manual-Gating-13.gif')
# Negated gates cyto_gate_draw(cs, alias = c("Dead Cells","Live Cells"), channels = c("Hoechst-405","Hoechst-430"), type = "rectangle", negate = TRUE, axes_trans = trans)
knitr::include_graphics('Gating/Manual-Gating-14.gif')
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