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06_conclusion.Rmd
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# smokingMouse
_Impartida por [Daianna González Padilla](https://daianna21.github.io/)_
* [Tutorial Expresión diferencial](http://research.libd.org/SPEAQeasyWorkshop2023/articles/SPEAQeasyWorkshop2023.html)
* Código: [LieberInstitute/smoking-nicotine-mouse](https://github.com/LieberInstitute/smoking-nicotine-mouse)
* Notas públicas de Daianna: [Notion](https://unequaled-boursin-0e1.notion.site/Modeling-the-effects-of-nicotine-and-smoking-exposures-on-the-developing-brain-85c9d6f413da4fd3a7dc1a5255f667d4).
# Revisión
* ¿Debemos explorar las relaciones entre nuestras variables con información de nuestras muestras previo a hacer un análisis de expresión diferencial?
* ¿Por qué usamos el paquete `edgeR`?
* ¿Por qué es importante el argumento `sort.by` en `topTable()`?
* ¿Por qué es importante el argumento `coef` en `topTable()`?
Usemos los datos de http://research.libd.org/SPEAQeasy-example/bootcamp_intro
```{r "speaqeasy_data"}
speaqeasy_data <- file.path(tempdir(), "rse_speaqeasy.RData")
download.file("https://github.com/LieberInstitute/SPEAQeasy-example/blob/master/rse_speaqeasy.RData?raw=true", speaqeasy_data, mode = "wb")
library("SummarizedExperiment")
load(speaqeasy_data, verbose = TRUE)
rse_gene
```
* ¿Cuantos genes y muestras tenemos en estos datos?
## Ejercicio en equipo
* ¿Hay diferencias en `totalAssignedGene` o `mitoRate` entre los grupos de diagnosis (`PrimaryDx`)?
* Grafica la expresión de _SNAP25_ para cada grupo de diagnosis.
* Sugiere un modelo estadistico que podríamos usar en una análisis de expresión diferencial. Verifica que si sea un modelo _full rank_. ¿Cúal sería el o los coeficientes de interés?
## Respuestas
```{r "respuestas"}
## Exploremos la variable de PrimaryDx
table(rse_gene$PrimaryDx)
## Eliminemos el diagnosis "Other" porque no tiene información
rse_gene$PrimaryDx <- droplevels(rse_gene$PrimaryDx)
table(rse_gene$PrimaryDx)
## Exploremos numéricamente diferencias entre grupos de diagnosis para
## varias variables
with(colData(rse_gene), tapply(totalAssignedGene, PrimaryDx, summary))
with(colData(rse_gene), tapply(mitoRate, PrimaryDx, summary))
## Podemos hacer lo mismo para otras variables
with(colData(rse_gene), tapply(mitoRate, BrainRegion, summary))
## Podemos resolver la primeras preguntas con iSEE
if (interactive()) iSEE::iSEE(rse_gene)
## O hacer graficas nosotros mismos. Aquí les muestro una posible respuesta
## con ggplot2
library("ggplot2")
ggplot(
as.data.frame(colData(rse_gene)),
aes(y = totalAssignedGene, group = PrimaryDx, x = PrimaryDx)
) +
geom_boxplot() +
theme_bw(base_size = 20) +
xlab("Diagnosis")
ggplot(
as.data.frame(colData(rse_gene)),
aes(y = totalAssignedGene, group = paste0(PrimaryDx, "_", BrainRegion), x = paste0(PrimaryDx, "_", BrainRegion))
) +
geom_boxplot() +
theme_bw(base_size = 20) +
xlab("Diagnosis")
ggplot(
as.data.frame(colData(rse_gene)),
aes(y = mitoRate, group = PrimaryDx, x = PrimaryDx)
) +
geom_boxplot() +
theme_bw(base_size = 20) +
xlab("Diagnosis")
ggplot(
as.data.frame(colData(rse_gene)),
aes(y = mitoRate, group = paste0(PrimaryDx, "_", BrainRegion), x = paste0(PrimaryDx, "_", BrainRegion))
) +
geom_boxplot() +
theme_bw(base_size = 20) +
xlab("Diagnosis")
## Otras variables
ggplot(
as.data.frame(colData(rse_gene)),
aes(y = mitoRate, group = BrainRegion, x = BrainRegion)
) +
geom_boxplot() +
theme_bw(base_size = 20) +
xlab("Brain Region")
## Encontremos el gene SNAP25
rowRanges(rse_gene)
## En este objeto los nombres de los genes vienen en la variable "Symbol"
i <- which(rowRanges(rse_gene)$Symbol == "SNAP25")
i
## Para graficar con ggplot2, hagamos un pequeño data.frame
df <- data.frame(
expression = assay(rse_gene)[i, ],
Dx = rse_gene$PrimaryDx
)
## Ya teniendo el pequeño data.frame, podemos hacer la gráfica
ggplot(df, aes(y = log2(expression + 0.5), group = Dx, x = Dx)) +
geom_boxplot() +
theme_bw(base_size = 20) +
xlab("Diagnosis") +
ylab("SNAP25: log2(x + 0.5)")
## https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/overview.html#3_Visualizing_expression_values
scater::plotExpression(
as(rse_gene, "SingleCellExperiment"),
features = rownames(rse_gene)[i],
x = "PrimaryDx",
exprs_values = "counts",
colour_by = "BrainRegion",
xlab = "Diagnosis"
)
if (requireNamespace("plotly", quietly = TRUE)) {
## Lo pueden instalar con
# install.packages("plotly")
## Guardemos el resultado de plotExpression()
p <- scater::plotExpression(
as(rse_gene, "SingleCellExperiment"),
features = rownames(rse_gene)[i],
x = "PrimaryDx",
exprs_values = "counts",
colour_by = "BrainRegion",
xlab = "Diagnosis"
)
## scater::plotExpression() regresa un objeto de clase ggplot
class(p)
## así que podemos usar plotly para crear una versión
## interactiva
plotly::ggplotly(p)
}
## Para el model estadístico exploremos la información de las muestras
colnames(colData(rse_gene))
## Podemos usar región del cerebro porque tenemos suficientes datos
table(rse_gene$BrainRegion)
## Pero no podemos usar "Race" porque son solo de 1 tipo
table(rse_gene$Race)
## Ojo! Acá es importante que hayamos usado droplevels(rse_gene$PrimaryDx)
## si no, vamos a tener un modelo que no sea _full rank_
mod <- with(
colData(rse_gene),
model.matrix(~ PrimaryDx + totalAssignedGene + mitoRate + rRNA_rate + BrainRegion + Sex + AgeDeath)
)
## Exploremos el modelo de forma interactiva
if (interactive()) {
## Tenemos que eliminar columnas que tienen NAs.
info_no_NAs <- colData(rse_gene)[, c(
"PrimaryDx", "totalAssignedGene", "rRNA_rate", "BrainRegion", "Sex",
"AgeDeath", "mitoRate", "Race"
)]
ExploreModelMatrix::ExploreModelMatrix(
info_no_NAs,
~ PrimaryDx + totalAssignedGene + mitoRate + rRNA_rate + BrainRegion + Sex + AgeDeath
)
## Veamos un modelo más sencillo sin las variables numéricas (continuas) porque
## ExploreModelMatrix nos las muestra como si fueran factors (categoricas)
## en vez de continuas
ExploreModelMatrix::ExploreModelMatrix(
info_no_NAs,
~ PrimaryDx + BrainRegion + Sex
)
## Si agregamos + Race nos da errores porque Race solo tiene 1 opción
# ExploreModelMatrix::ExploreModelMatrix(
# info_no_NAs,
# ~ PrimaryDx + BrainRegion + Sex + Race
# )
}
```
¿Quieres más datos? Tenemos muchos en LIBD incluyendo http://eqtl.brainseq.org/phase2/.
# R/Bioconductor-powered Team Data Science
https://lcolladotor.github.io/
<iframe width="560" height="315" src="https://www.youtube.com/embed/33scakbTNO0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<script async class="speakerdeck-embed" data-id="3c32410b600740abb4724486e83ebd30" data-ratio="1.77725118483412" src="//speakerdeck.com/assets/embed.js"></script>
# spatialLIBD
<blockquote class="twitter-tweet"><p lang="en" dir="ltr">🔥off the press! 👀 our <a href="https://twitter.com/biorxivpreprint?ref_src=twsrc%5Etfw">@biorxivpreprint</a> on human 🧠brain <a href="https://twitter.com/LieberInstitute?ref_src=twsrc%5Etfw">@LieberInstitute</a> spatial 🌌🔬transcriptomics data 🧬using Visium <a href="https://twitter.com/10xGenomics?ref_src=twsrc%5Etfw">@10xGenomics</a>🎉<a href="https://twitter.com/hashtag/spatialLIBD?src=hash&ref_src=twsrc%5Etfw">#spatialLIBD</a><br><br>🔍<a href="https://t.co/RTW0VscUKR">https://t.co/RTW0VscUKR</a> <br>👩🏾💻<a href="https://t.co/bsg04XKONr">https://t.co/bsg04XKONr</a><br>📚<a href="https://t.co/FJDOOzrAJ6">https://t.co/FJDOOzrAJ6</a><br>📦<a href="https://t.co/Au5jwADGhY">https://t.co/Au5jwADGhY</a><a href="https://t.co/PiWEDN9q2N">https://t.co/PiWEDN9q2N</a> <a href="https://t.co/aWy0yLlR50">pic.twitter.com/aWy0yLlR50</a></p>— 🇲🇽 Leonardo Collado-Torres (@lcolladotor) <a href="https://twitter.com/lcolladotor/status/1233661576433061888?ref_src=twsrc%5Etfw">February 29, 2020</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
<script defer class="speakerdeck-embed" data-id="2c3377401c934bb9abd859b644bb9455" data-ratio="1.7772511848341233" src="//speakerdeck.com/assets/embed.js"></script>
Diapositivas de mis pláticas anteriores están disponibles en https://speakerdeck.com/lcolladotor.
* Platicas grabadas
Usta es la versión de un webinar para [BioTuring](https://bioturing.com/) que pueden ver a través de YouTube
<iframe width="560" height="315" src="https://www.youtube.com/embed/S8884Kde-1U" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
Aquí hay una versión anterior:
<iframe width="560" height="315" src="https://www.youtube.com/embed/aD2JU-vUv54" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
* Artículo: https://www.nature.com/articles/s41593-020-00787-0
* Software: http://research.libd.org/spatialLIBD/ o `r BiocStyle::Biocpkg("spatialLIBD")`
* Interfaz de shiny: http://spatial.libd.org/spatialLIBD/
* Libro (en construcción) donde explicamos como usar varias herramientas: https://lmweber.org/BestPracticesST/
* Artículo sobre `SpatialExperiment` http://dx.doi.org/10.1093/bioinformatics/btac299
<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Are you working with spatial transcriptomics data such as Visium from <a href="https://twitter.com/10xGenomics?ref_src=twsrc%5Etfw">@10xGenomics</a>? Then you'll be interested in <a href="https://twitter.com/hashtag/SpatialExperiment?src=hash&ref_src=twsrc%5Etfw">#SpatialExperiment</a> 📦 led by <a href="https://twitter.com/drighelli?ref_src=twsrc%5Etfw">@drighelli</a> <a href="https://twitter.com/lmwebr?ref_src=twsrc%5Etfw">@lmwebr</a> <a href="https://twitter.com/CrowellHL?ref_src=twsrc%5Etfw">@CrowellHL</a> with contributions by <a href="https://twitter.com/PardoBree?ref_src=twsrc%5Etfw">@PardoBree</a> <a href="https://twitter.com/shazanfar?ref_src=twsrc%5Etfw">@shazanfar</a> A Lun <a href="https://twitter.com/stephaniehicks?ref_src=twsrc%5Etfw">@stephaniehicks</a> <a href="https://twitter.com/drisso1893?ref_src=twsrc%5Etfw">@drisso1893</a> 🌟<br><br>📜 <a href="https://t.co/r36qlakRJe">https://t.co/r36qlakRJe</a> <a href="https://t.co/cWIiwLFitV">pic.twitter.com/cWIiwLFitV</a></p>— 🇲🇽 Leonardo Collado-Torres (@lcolladotor) <a href="https://twitter.com/lcolladotor/status/1355208674856329218?ref_src=twsrc%5Etfw">January 29, 2021</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
Brenda Pardo
https://twitter.com/PardoBree
<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Today I gave my first talk at a congress in <a href="https://twitter.com/hashtag/EuroBioc2020?src=hash&ref_src=twsrc%5Etfw">#EuroBioc2020</a> about our work on adapting the package <a href="https://twitter.com/hashtag/spatialLIBD?src=hash&ref_src=twsrc%5Etfw">#spatialLIBD</a> to use VisiumExperiment objects. <a href="https://t.co/U23yE32RWM">pic.twitter.com/U23yE32RWM</a></p>— Brenda Pardo (@PardoBree) <a href="https://twitter.com/PardoBree/status/1338560370382942209?ref_src=twsrc%5Etfw">December 14, 2020</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Our paper describing our package <a href="https://twitter.com/hashtag/spatialLIBD?src=hash&ref_src=twsrc%5Etfw">#spatialLIBD</a> is finally out! 🎉🎉🎉<br><br>spatialLIBD is an <a href="https://twitter.com/hashtag/rstats?src=hash&ref_src=twsrc%5Etfw">#rstats</a> / <a href="https://twitter.com/Bioconductor?ref_src=twsrc%5Etfw">@Bioconductor</a> package to visualize spatial transcriptomics data.<br>⁰<br>This is especially exciting for me as it is my first paper as a first author 🦑.<a href="https://t.co/COW013x4GA">https://t.co/COW013x4GA</a><br><br>1/9 <a href="https://t.co/xevIUg3IsA">pic.twitter.com/xevIUg3IsA</a></p>— Brenda Pardo (@PardoBree) <a href="https://twitter.com/PardoBree/status/1388253938391175173?ref_src=twsrc%5Etfw">April 30, 2021</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
# Comunidad
* https://twitter.com/miR_community
* https://twitter.com/R_LGBTQ
* https://twitter.com/conecta_R
* https://twitter.com/LatinR_Conf
* https://twitter.com/R4DScommunity
* https://twitter.com/RConsortium
* https://twitter.com/rweekly_org
* https://twitter.com/RLadiesGlobal
* https://twitter.com/RLadiesBmore
* https://twitter.com/search?q=%23RLadiesMX&src=typed_query
<blockquote class="twitter-tweet"><p lang="en" dir="ltr">The blog post about the First annual meeting of <a href="https://twitter.com/hashtag/RLadiesMX?src=hash&ref_src=twsrc%5Etfw">#RLadiesMX</a> is ready!! All <a href="https://twitter.com/hashtag/rladies?src=hash&ref_src=twsrc%5Etfw">#rladies</a> chapters in México met for the first time! 🤩 Spread the word and join this amazing community 💜<a href="https://t.co/evY4Tc18rw">https://t.co/evY4Tc18rw</a> Thanks <a href="https://twitter.com/AnaBetty2304?ref_src=twsrc%5Etfw">@AnaBetty2304</a> <a href="https://twitter.com/Averi_GG?ref_src=twsrc%5Etfw">@Averi_GG</a> and <a href="https://twitter.com/josschavezf1?ref_src=twsrc%5Etfw">@josschavezf1</a> for all your work!</p>— RLadies Cuernavaca (@RLadiesCuerna) <a href="https://twitter.com/RLadiesCuerna/status/1355655180751151107?ref_src=twsrc%5Etfw">January 30, 2021</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
* https://twitter.com/Bioconductor
* https://twitter.com/rOpenSci
* https://twitter.com/LIBDrstats
* https://twitter.com/CDSBMexico
<blockquote class="twitter-tweet"><p lang="es" dir="ltr">¡Chequen el nuevo blog post de Erick <a href="https://twitter.com/ErickCuevasF?ref_src=twsrc%5Etfw">@ErickCuevasF</a>! 💯<br><br>Nos describe sus experiencias en <a href="https://twitter.com/hashtag/BioC2020?src=hash&ref_src=twsrc%5Etfw">#BioC2020</a> y <a href="https://twitter.com/hashtag/CDSB2020?src=hash&ref_src=twsrc%5Etfw">#CDSB2020</a><br><br>Además estamos orgullxs de que Erick se unió a la Junta Directiva de la CDSB 🤩🎉<br><br>👀 <a href="https://t.co/uGpgnqXvVM">https://t.co/uGpgnqXvVM</a><a href="https://twitter.com/hashtag/rstatsES?src=hash&ref_src=twsrc%5Etfw">#rstatsES</a> <a href="https://t.co/O2eIbk5YoZ">pic.twitter.com/O2eIbk5YoZ</a></p>— ComunidadBioInfo (@CDSBMexico) <a href="https://twitter.com/CDSBMexico/status/1296920807105540098?ref_src=twsrc%5Etfw">August 21, 2020</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
## De alumnos LCG 2021
<blockquote class="twitter-tweet"><p lang="en" dir="ltr"><a href="https://twitter.com/fikandata?ref_src=twsrc%5Etfw">@fikandata</a> <a href="https://twitter.com/MqElizabeth?ref_src=twsrc%5Etfw">@MqElizabeth</a> <br><br>Looking for a solid and useful R 📦, we stumbled upon this <br>beauty 🤩 <a href="https://t.co/KR3twAxqRY">https://t.co/KR3twAxqRY</a><br><br>shoutouts to <a href="https://twitter.com/digitalwright?ref_src=twsrc%5Etfw">@digitalwright</a> 👈!!<a href="https://twitter.com/lcolladotor?ref_src=twsrc%5Etfw">@lcolladotor</a> <a href="https://twitter.com/Bioconductor?ref_src=twsrc%5Etfw">@Bioconductor</a></p>— Axel Zagal Norman (@NormanZagal) <a href="https://twitter.com/NormanZagal/status/1364381133878611968?ref_src=twsrc%5Etfw">February 24, 2021</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
<blockquote class="twitter-tweet"><p lang="en" dir="ltr">In today's lesson of bioinformatics course of undergraduate program in genomic sciences <a href="https://twitter.com/lcgunam?ref_src=twsrc%5Etfw">@lcgunam</a> we created our first personal page using <a href="https://twitter.com/seankross?ref_src=twsrc%5Etfw">@seankross</a>' postcards R package with <a href="https://twitter.com/lcolladotor?ref_src=twsrc%5Etfw">@lcolladotor</a> as our instructor. <a href="https://twitter.com/hashtag/rstats?src=hash&ref_src=twsrc%5Etfw">#rstats</a> <a href="https://t.co/sXUSietCZy">https://t.co/sXUSietCZy</a></p>— Angel Castillo (@angelcaztle13) <a href="https://twitter.com/angelcaztle13/status/1364466027682140162?ref_src=twsrc%5Etfw">February 24, 2021</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Wake up <br>Brew some <a href="https://twitter.com/tyulmalcafe?ref_src=twsrc%5Etfw">@tyulmalcafe</a> beans <br>Attend <a href="https://twitter.com/lcolladotor?ref_src=twsrc%5Etfw">@lcolladotor</a> amazing class on visualizing expression data using ISEE <a href="https://twitter.com/FedeBioinfo?ref_src=twsrc%5Etfw">@FedeBioinfo</a> <a href="https://twitter.com/KevinRUE67?ref_src=twsrc%5Etfw">@KevinRUE67</a> <a href="https://twitter.com/CSoneson?ref_src=twsrc%5Etfw">@CSoneson</a> <br>Am I dreaming? <br>Nah! Mug is empty.</p>— Alfredo Varela (@fikandata) <a href="https://twitter.com/fikandata/status/1364669473634983941?ref_src=twsrc%5Etfw">February 24, 2021</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Today I learned how to visualize data in a cool and easy way in <a href="https://twitter.com/lcolladotor?ref_src=twsrc%5Etfw">@lcolladotor</a> 's class. <br><br>ExploreModelMatrix definitely makes your life easier! <br>Shoutouts to:<a href="https://twitter.com/CSoneson?ref_src=twsrc%5Etfw">@CSoneson</a> <a href="https://twitter.com/FedeBioinfo?ref_src=twsrc%5Etfw">@FedeBioinfo</a> <a href="https://twitter.com/mikelove?ref_src=twsrc%5Etfw">@mikelove</a></p>— Axel Zagal Norman (@NormanZagal) <a href="https://twitter.com/NormanZagal/status/1365034931261349889?ref_src=twsrc%5Etfw">February 25, 2021</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
## De ustedes
??