Selected examples of inter-individual heterogeneity
Anthony Hung
2021-01-21
Last updated: 2021-01-21
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Knit directory: invitroOA_pilot_repository/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | e3fbd0f | Anthony Hung | 2021-01-21 | add ward et al data files to data |
| html | e3fbd0f | Anthony Hung | 2021-01-21 | add ward et al data files to data |
Introduction
Here, we plot the expression values of three genes for which we identified inter-individual hetereogeneity in the response to mechanical strain.
Load data and libraries
library(ggplot2)
#load in V2 results from voom in DE analysis
v2 <- readRDS("output/voom_results.rds")Plot a dot plot for each of the three genes
# this function takes in the v2 object and the name of a gene (Ensmbl ID) and outputs a plot
plot_gene <- function(v, g) {
# v - An EList object containing log2 counts per million
# g - character vector of a single gene
stopifnot(class(v) == "EList",
is.character(g), length(g) == 1)
library("tidyr")
single_gene <- v$E[g, ]
single_gene_long <- as.data.frame(single_gene)
colnames(single_gene_long) <- "log2cpm"
single_gene_long$sample <- rownames(single_gene_long)
single_gene_long <- separate(single_gene_long, col = "sample", sep = "_",
into = c("Individual", "Replicate", "Treatment"))
single_gene_long$Treatment <- gsub('S', 'Strain', single_gene_long$Treatment)
single_gene_long$Treatment <- gsub('U', 'Control', single_gene_long$Treatment)
single_gene_long$Treatment <- factor(single_gene_long$Treatment, levels(factor(single_gene_long$Treatment))[c(1,2)])
return(ggplot(single_gene_long, aes(x = Individual, y = log2cpm, fill = Individual)) +
labs(title = g, y = expression("Expression level (" * log[2] * " cpm)")) +
geom_dotplot(binaxis = "y", stackdir = "center", key_glyph = 'rect', dotsize = 0.75) +
facet_wrap(~Treatment, strip.position = 'bottom') +
stat_summary(fun.data = "mean_sdl", fun.args = list(mult=1)) +
theme(axis.title.x=element_blank())
)
}Make plots
gene_list <- c("ENSG00000157227", "ENSG00000181789", "ENSG00000120699")
for (gene in gene_list) {
print(plot_gene(v2, as.character(gene)))
}Loading required package: limma`stat_bindot()` using `bins = 30`. Pick better value with `binwidth`.
| Version | Author | Date |
|---|---|---|
| e3fbd0f | Anthony Hung | 2021-01-21 |
`stat_bindot()` using `bins = 30`. Pick better value with `binwidth`.
| Version | Author | Date |
|---|---|---|
| e3fbd0f | Anthony Hung | 2021-01-21 |
`stat_bindot()` using `bins = 30`. Pick better value with `binwidth`.
| Version | Author | Date |
|---|---|---|
| e3fbd0f | Anthony Hung | 2021-01-21 |
sessionInfo()R version 3.6.3 (2020-02-29)
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] limma_3.40.6 tidyr_1.1.2 ggplot2_3.3.2
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.16 purrr_0.3.4
[4] splines_3.6.3 lattice_0.20-41 colorspace_1.4-1
[7] vctrs_0.3.4 generics_0.0.2 htmltools_0.5.0
[10] yaml_2.2.1 base64enc_0.1-3 survival_3.2-3
[13] rlang_0.4.7 later_1.1.0.1 pillar_1.4.6
[16] foreign_0.8-75 glue_1.4.2 withr_2.2.0
[19] RColorBrewer_1.1-2 jpeg_0.1-8.1 lifecycle_0.2.0
[22] stringr_1.4.0 munsell_0.5.0 gtable_0.3.0
[25] workflowr_1.6.2 htmlwidgets_1.5.1 evaluate_0.14
[28] labeling_0.3 latticeExtra_0.6-29 knitr_1.29
[31] httpuv_1.5.4 htmlTable_2.0.1 Rcpp_1.0.5
[34] checkmate_2.0.0 promises_1.1.1 scales_1.1.1
[37] backports_1.1.9 Hmisc_4.4-1 farver_2.0.3
[40] fs_1.5.0 gridExtra_2.3 png_0.1-7
[43] digest_0.6.25 stringi_1.4.6 dplyr_1.0.2
[46] grid_3.6.3 rprojroot_1.3-2 tools_3.6.3
[49] magrittr_1.5 tibble_3.0.3 Formula_1.2-3
[52] cluster_2.1.0 crayon_1.3.4 whisker_0.4
[55] pkgconfig_2.0.3 ellipsis_0.3.1 Matrix_1.2-18
[58] data.table_1.12.8 rmarkdown_2.3 rstudioapi_0.11.0-9000
[61] R6_2.4.1 rpart_4.1-15 nnet_7.3-14
[64] git2r_0.27.1 compiler_3.6.3