GoM DE analysis of droplet data
Peter Carbonetto
Last updated: 2022-02-10
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Knit directory: single-cell-topics/analysis/
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| Rmd | 7742b51 | Peter Carbonetto | 2022-02-10 | workflowr::wflow_publish(“de_analysis_droplet.Rmd”) |
| html | 6542952 | Peter Carbonetto | 2022-02-07 | Create droplet volcano plots for paper in de_analysis_droplet analysis. |
| Rmd | 726bd7a | Peter Carbonetto | 2022-02-07 | workflowr::wflow_publish(“de_analysis_droplet.Rmd”, verbose = TRUE) |
| html | cdfb0dc | Peter Carbonetto | 2022-02-07 | Added volcano plots to de_analysis_droplet analysis. |
| Rmd | 0796a94 | Peter Carbonetto | 2022-02-07 | workflowr::wflow_publish(“de_analysis_droplet.Rmd”, verbose = TRUE) |
| Rmd | 6499def | Peter Carbonetto | 2022-02-02 | Working on exploratory analysis de_analysis_pulseseq.R. |
| html | 124013c | Peter Carbonetto | 2022-01-30 | Revised the de_analysis_droplet volcano plots. |
| Rmd | 154843c | Peter Carbonetto | 2022-01-30 | workflowr::wflow_publish(“de_analysis_droplet.Rmd”) |
| Rmd | c0803ab | Peter Carbonetto | 2022-01-30 | A couple small edits. |
| html | 515f2b2 | Peter Carbonetto | 2022-01-30 | First build of de_analysis_droplet page. |
| Rmd | b08d530 | Peter Carbonetto | 2022-01-30 | workflowr::wflow_publish(“de_analysis_droplet.Rmd”) |
| Rmd | 618a9e2 | Peter Carbonetto | 2022-01-30 | workflowr::wflow_publish(“index.Rmd”) |
Here we summarize the results of performing DE analysis on the droplet data using the topic model with \(K = 7\) topics.
Load the packages used in the analysis.
library(fastTopics)
library(ggplot2)
library(cowplot)Load the results of the differential expression analysis.
load("../output/droplet/de-droplet.RData")For reference, here is the Structure plot from an earlier analysis of the droplet data:
These volcano plots summarize the results off the DE analysis after merging topics 5 and 7:
p1 <- volcano_plot(de_merged,ymax = 100,k = "k1")
p2 <- volcano_plot(de_merged,ymax = 200,k = "k2")
p3 <- volcano_plot(de_merged,ymax = 200,k = "k3")
p4 <- volcano_plot(de_merged,ymax = 200,k = "k4")
p5 <- volcano_plot(de_merged,ymax = 200,k = "k5+k7")
p6 <- volcano_plot(de_merged,ymax = 100,k = "k6")
plot_grid(p1,p2,p3,p4,p5,p6,nrow = 3,ncol = 2)
Judging by the most overexpressed genes in these volcano plots, the topics capture goblet cells (topic 1), basal cells (topic 2), “hillock” club cells (topic 4), ciliated, tuft and neuroendocrine cells (topic 6), and club cells (topics 5 + 7).
Topic 7 is driven by variation in expression of Scgb1a1 in club cells:
p7 <- volcano_plot(de,k = "k5",ymax = 200)
p8 <- volcano_plot(de,k = "k7",ymax = 200)
plot_grid(p7,p8)
These same results can also be explored in interactive volcano plots:
volcano_plotly(de_merged,k = "k1",ymax = 100,
file = "volcano_plot_droplet_goblet.html",
width = 600,height = 600)
volcano_plotly(de_merged,k = "k2",ymax = 200,
file = "volcano_plot_droplet_basal.html",
width = 600,height = 600)
volcano_plotly(de_merged,k = "k3",ymax = 200,
file = "volcano_plot_droplet_k3.html",
width = 600,height = 600)
volcano_plotly(de_merged,k = "k4",ymax = 200,
file = "volcano_plot_droplet_hillock.html",
width = 600,height = 600)
volcano_plotly(de_merged,k = "k5+k7",ymax = 200,
file = "volcano_plot_droplet_club.html",
width = 600,height = 600)
volcano_plotly(de_merged,k = "k6",ymax = 100,
file = "volcano_plot_droplet_rare.html",
width = 600,height = 600)
volcano_plotly(de,k = "k5",ymax = 200,
file = "volcano_plot_droplet_club_splunc1.html",
width = 600,height = 600)
volcano_plotly(de,k = "k7",ymax = 200,
file = "volcano_plot_droplet_club_scgb1a1.html",
width = 600,height = 600)You can explore these interactive volcano plots by following these links:
sessionInfo()
# R version 3.6.2 (2019-12-12)
# Platform: x86_64-apple-darwin15.6.0 (64-bit)
# Running under: macOS Catalina 10.15.7
#
# Matrix products: default
# BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
#
# locale:
# [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] cowplot_1.0.0 ggplot2_3.3.5 fastTopics_0.6-98
#
# loaded via a namespace (and not attached):
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