Retrofit Colon Vignette
2024-10-29
Contents
- 1 Introduction
- 2 Package Installation and other requirements
- 3 Spatial Transcriptomics Data
- 4 Reference-free Deconvolution
- 5 Cell-type Annotation via annotated single-cell reference
- 6 Cell-type Annotation via known marker genes
- 7 Results and visualization
- 7.1 Figure 4A: Proportion of different cell types in the tissue.
- 7.2 Figure 4C: Localization of cell types with the dominant cell type in each spot
- 7.3 Figure 4D: Gene expression of Epithelial marker genes across spots
- 7.4 Figure 4E: Proportion of Epithelial cells across spots
- 7.5 Figure 5A: Proportion of different cell types in different spots
- 7.6 Figure 5D: Spots with 1 dominant cell type i.e., proportion > 0.5
- 7.7 Figure 5E: Co-localized spots for Epithelial cells
- 7.8 Figure 6C: Concordance between expression profiles of found genes obtained from RETROFIT and scRNA-seq data
- 8 Session information
1 Introduction
RETROFIT is a statistical method for reference-free deconvolution of spatial transcriptomics data to estimate cell type mixtures. In this Vignette, we will estimate cell type composition of a Colon dataset. We will annotate cell types using marker gene lists as well as single cell reference. We will also reproduce some of the results from the paper for illustration.
2 Package Installation and other requirements
Install and load the packages using the following steps:
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("retrofit")library(retrofit)3 Spatial Transcriptomics Data
First load the Colon ST data from fetal 12 PCW tissue, using the following command:
data("vignetteColonData")
X = vignetteColonData$a3_x4 Reference-free Deconvolution
Initialize the required parameters for deconvolution. - iterations: Number of iterations (default = 4000) - L: Number of components required
iterations = 10
L = 20After initialization, run retrofit on the data (X) as follows:
result = retrofit::decompose(X, L=L, iterations=iterations, verbose=TRUE)## [1] "iteration: 1 0.143 Seconds"
## [1] "iteration: 2 0.143 Seconds"
## [1] "iteration: 3 0.144 Seconds"
## [1] "iteration: 4 0.178 Seconds"
## [1] "iteration: 5 0.156 Seconds"
## [1] "iteration: 6 0.151 Seconds"
## [1] "iteration: 7 0.154 Seconds"
## [1] "iteration: 8 0.144 Seconds"
## [1] "iteration: 9 0.144 Seconds"
## [1] "iteration: 10 0.165 Seconds"
## [1] "Iteration mean: 0.152 seconds total: 1.521 seconds"H = result$h
W = result$w
Th = result$thAfter deconvolution of ST data, we have our estimates of W (a matrix of order G x L), H (a matrix of order L x S) and Theta (a vector of L components). Here, we are using number of iterations as 20 for demonstration purposes. For reproducing results in the paper, we need to run RETROFIT for iterations = 4000. The whole computation is omitted here due to time complexity (> 10min). We will load the results from 4000 iterations for the rest of the analysis.
H = vignetteColonData$a3_results_4k_iterations$decompose$h
W = vignetteColonData$a3_results_4k_iterations$decompose$w
Th = vignetteColonData$a3_results_4k_iterations$decompose$thAbove results are obtained by running the code below.
iterations = 4000
set.seed(1)
result = retrofit::decompose(x, L=L, iterations=iterations)Next, we need to annotate the components, to get the proportion of K cell types. We can do this in two ways: (a) using an annotated single cell reference or (b) using the known marker genes.
5 Cell-type Annotation via annotated single-cell reference
Here, we will annotate components using single-cell reference. Load the single-cell reference data:
sc_ref = vignetteColonData$sc_refThis file contains average gene expression values for K=8 cell types. Run the following command to get K cell-type mixtures from the ST data X:
K = ncol(sc_ref) # number of cell types
result = annotateWithCorrelations(sc_ref, K, W, H)
H_sc = result$h
W_sc = result$w
H_sc_prop = result$h_prop
W_sc_prop = result$w_propWe assign components to the cell type it has maximum correlation with as shown in figure above. Finally, cell-type proportions for each spot in the ST data (X) are stored in H_mark_prop of order K x S. You can verify that the mappings from both methods are largely similar.
W_norm <- W
for(i in 1:nrow(W)){
W_norm[i,]=W[i,]/sum(W[i,])
}
corrplot::corrplot(stats::cor(sc_ref, W_norm),
is.corr=FALSE,
mar=c(0,0,1,0),
col = colorRampPalette(c("white", "deepskyblue", "blue4"))(100),
main="Correlation-based Mapping Matrix")
6 Cell-type Annotation via known marker genes
Here, we will annotate using known marker genes for cell types. Load the marker gene list:
marker_ref = vignetteColonData$marker_refThis file contains the list of marker genes for K = 8 cell types. Run the following command to get K cell-type mixtures from the ST data X:
K = length(marker_ref) # number of cell types
result = retrofit::annotateWithMarkers(marker_ref, K, W, H)
H_mark = result$h
W_mark = result$w
H_mark_prop = result$h_prop
W_mark_prop = result$w_prop
gene_sums = result$gene_sumscorrplot::corrplot(gene_sums,
is.corr=FALSE,
mar=c(0,0,1,0),
col=colorRampPalette(c("white", "deepskyblue", "blue4"))(100),
main="Marker-based Mapping Matrix")
We assign components to the cell type it has maximum average marker expression in, as shown in figure above. Finally, cell-type proportions for each spot in the ST data (X) are stored in H_est of order K x S.
7 Results and visualization
Hereon, we will be reproducing some of the analysis from the paper using marker-based mapping results.
7.1 Figure 4A: Proportion of different cell types in the tissue.
Proportion of cell-types in this tissue:
rowSums(H_mark_prop)/ncol(H_mark_prop)## Endothelium Epithelial Fibroblasts Immune Muscle Myo.Meso
## 0.13018273 0.13980586 0.24423669 0.09745911 0.12181790 0.10049303
## Neural Pericytes
## 0.09560567 0.070399027.2 Figure 4C: Localization of cell types with the dominant cell type in each spot
Load the coordinates for the spots in the tissue and the tissue image:
coords=vignetteColonData$a3_coords
img <- png::readPNG(RCurl::getURLContent("https://user-images.githubusercontent.com/90921267/210159136-96b56551-f414-4b0b-921e-98f05a98c8bc.png"))
t <- grid::rasterGrob(img, width=ggplot2::unit(1,"npc"), height=ggplot2::unit(1,"npc"), interpolate = FALSE)Find the cell-type with maximum proportion in each spot and plot:
dat=as.data.frame(cbind(coords,t(H_mark_prop)))
colnames(dat)=c(colnames(coords),rownames(H_mark_prop))
df=dat[,-c(1:3)]
df$CellType=NA
for(i in 1:nrow(df)){
df$CellType[i]=names(which.max(df[i,-c(1:2)]))
}
df$CellType=factor(df$CellType,levels=c("Epithelial", "Immune", "Myo.Meso","Muscle",
"Neural", "Endothelium", "Pericytes","Fibroblasts"))
ggplot2::ggplot(df, ggplot2::aes(x=imagerow, y=imagecol)) +
ggplot2::geom_point(size=1.8, shape=21, ggplot2::aes(fill=CellType))+
ggplot2::scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9","#009E73", "#CC79A7",
"#0072B2", "#D55E00" ,"#F0E442"),
labels=c("Epithelial", "Immune","Myofibroblasts/\nMesothelium",
"Muscle","Neural","Endothelium",
"Pericytes","Fibroblasts"))+
ggplot2::xlab("") + ggplot2::ylab("") + ggplot2::theme_classic()+
ggplot2::theme(legend.position = "none",
axis.line = ggplot2::element_blank(),
plot.margin = ggplot2::margin(-0.2, -0.2, 0.2, -1, "cm"),
axis.text.x = ggplot2::element_blank(), axis.text.y = ggplot2::element_blank(),
axis.ticks.x = ggplot2::element_blank(), axis.ticks.y = ggplot2::element_blank()) 
7.3 Figure 4D: Gene expression of Epithelial marker genes across spots
Plot the spatial expression for Epithelial markers:
df = as.data.frame(cbind(coords, t(X[marker_ref$Epithelial,])))
df$metagene = unname(rowSums(df[,-c(1:5)]))
df$metagene[df$metagene>quantile(df$metagene,0.95)]=quantile(df$metagene,0.95)
ggplot2::ggplot(df, ggplot2::aes(x=imagerow, y=imagecol)) +
# ggplot2::annotation_custom(t, 700, 6400, 990, 6550) +
ggplot2::geom_point(size=1.5, ggplot2::aes(color=metagene))+
ggplot2::scale_color_gradientn(name="Epithelial Markers ",
colors=colorspace::adjust_transparency("grey20",
alpha = c(0,0.5,1)),
n.breaks=3) +
ggplot2::xlab("") + ggplot2::ylab("") +
ggplot2::theme_classic()+
ggplot2::theme(legend.key.height = ggplot2::unit(0.2, 'cm'), #change legend key size
legend.key.width = ggplot2::unit(0.8, 'cm'),
legend.title = ggplot2::element_text(size=10),
legend.position = "bottom",
legend.box.margin=ggplot2::margin(-20,-10,-5,-10),
plot.margin = ggplot2::margin(-0.2, -0.2, 0.2, -1, "cm"),
axis.line=ggplot2::element_blank(),
legend.text=ggplot2::element_text(size=8),
axis.text.x = ggplot2::element_blank(),
axis.text.y = ggplot2::element_blank(),
axis.ticks.x=ggplot2::element_blank(),
axis.ticks.y=ggplot2::element_blank())
7.4 Figure 4E: Proportion of Epithelial cells across spots
Plot the estimated proportions for Epithelial cell-type:
df=dat[,-c(1:3)]
ggplot2::ggplot(df, ggplot2::aes(x=imagerow, y=imagecol)) +
# ggplot2::annotation_custom(t, 700, 6400, 990, 6550) +
ggplot2::geom_point(size=1.5, ggplot2::aes(color=Epithelial))+
ggplot2::scale_color_gradientn(name="Epithelial ",
colors=colorspace::adjust_transparency("grey20",
alpha = c(0,0.5,1)),
n.breaks=3, limits=c(0,1)) +
ggplot2::xlab("") + ggplot2::ylab("") +
ggplot2::theme_classic()+
ggplot2::theme(legend.key.height = ggplot2::unit(0.2, 'cm'), #change legend key size
legend.key.width = ggplot2::unit(0.8, 'cm'),
legend.title = ggplot2::element_text(size=10),
legend.position = "bottom",
legend.box.margin=ggplot2::margin(-20,-10,-5,-10),
plot.margin = ggplot2::margin(-0.2, -0.2, 0.2, -1, "cm"),
axis.line=ggplot2::element_blank(),
legend.text=ggplot2::element_text(size=8),
axis.text.x = ggplot2::element_blank(), axis.text.y = ggplot2::element_blank(),
axis.ticks.x=ggplot2::element_blank(),axis.ticks.y=ggplot2::element_blank())
Verify that the spatial pattern exhibited by the epithelial markers is largely similar to that of the estimated proportion for epithelial cells.
7.5 Figure 5A: Proportion of different cell types in different spots
Visualize the proportion of different cell types and colocalization patterns:
## Structure Plots
plotfn <- function(df=NULL)
{
#reshape to long format
df$num <- 1:nrow(df)
df1 <- reshape2::melt(df,id.vars = "num")
#reversing order for cosmetic reasons
df1 <- df1[rev(1:nrow(df1)),]
#plot
p <- ggplot2::ggplot(df1, ggplot2::aes(x=num,y=value,fill=variable))+
ggplot2::geom_bar(stat="identity",position="fill",width = 1, space = 0)+
ggplot2::scale_x_continuous(expand = c(0, 0))+
ggplot2::scale_y_continuous(expand = c(0, 0))+
ggplot2::labs(x = NULL, y = NULL)+
ggplot2::theme_grey(base_size=7)+
ggplot2::theme(legend.text = ggplot2::element_text(size = 20),legend.position = "bottom",
legend.key.size = ggplot2::unit(0.4, "cm"),
legend.title = ggplot2::element_blank(),
axis.ticks = ggplot2::element_blank(),
axis.text.y = ggplot2::element_text(size = 15),
axis.text.x = ggplot2::element_blank())+
ggplot2::scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9",
"#009E73", "#CC79A7", "#0072B2",
"#D55E00", "#F0E442"))
p
}
df=as.data.frame(t(H_mark_prop[c(2,4,6,5,7,1,8,3),]))
#pick max cluster, match max to cluster
maxval <- apply(df,1,max)
matchval <- vector(length=nrow(df))
for(j in 1:nrow(df)) matchval[j] <- match(maxval[j],df[j,])
#add max and match to df
df_q <- df
df_q$maxval <- maxval
df_q$matchval <- matchval
#order dataframe ascending match and decending max
df_q <- df_q[with(df_q, order(matchval,-maxval)), ]
#remove max and match
df_q$maxval <- NULL
df_q$matchval <- NULL
plotfn(df=df_q)+
ggplot2::theme(legend.position="bottom")+
ggplot2::ggtitle("Fetal 12 PCW (B)")+
ggplot2::theme(plot.title = ggplot2::element_text(hjust=0.5,size=25))
7.6 Figure 5D: Spots with 1 dominant cell type i.e., proportion > 0.5
Plot the proportion of only dominant cell types i.e., cell types with proportion > 0.5 in a spot.
df=dat
df_new=df[df$Epithelial>0.5 | df$Fibroblasts>0.5 | df$Myo.Meso>0.5 |
df$Endothelium>0.5 | df$Pericytes>0.5 | df$Neural>0.5 |
df$Immune>0.5 | df$Muscle>0.5,-c(1:3)]
df_new$CellType=1*(df_new$Epithelial>0.5) + 2*(df_new$Immune>0.5) +
3*(df_new$Myo.Meso>0.5) + 4*(df_new$Muscle>0.5) + 5*(df_new$Neural>0.5)+
6*(df_new$Endothelium>0.5) + 7*(df_new$Pericytes>0.5) + 8*(df_new$Fibroblasts>0.5)
df_new$CellType=factor(df_new$CellType)
ggplot2::ggplot(df_new, ggplot2::aes(x=imagerow, y=imagecol)) +
# ggplot2::annotation_custom(t, 700, 6400, 990, 6550) +
ggplot2::geom_point(size=1.8, shape=21, ggplot2::aes(fill=CellType))+
ggplot2::scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9",
"#009E73", "#CC79A7", "#0072B2",
"#D55E00", "#F0E442"),
labels=c("Epithelial","Immune",
"Myofibroblasts\nMesothelium",
"Muscle", "Neural", "Endothelium",
"Pericytes", "Fibroblasts"))+
ggplot2::xlab("") + ggplot2::ylab("") +
ggplot2::theme_classic()+
ggplot2::theme(legend.key.height = ggplot2::unit(0.5, 'cm'), #change legend key size
legend.key.width = ggplot2::unit(1, 'cm'),
legend.title = ggplot2::element_blank(),
legend.position = "none",
plot.margin = ggplot2::margin(-0.2, -0.2, 0.2, -1, "cm"),
axis.line=ggplot2::element_blank(),
legend.text=ggplot2::element_text(size=9),
axis.text.x = ggplot2::element_blank(), axis.text.y = ggplot2::element_blank(),
axis.ticks.x=ggplot2::element_blank(),axis.ticks.y=ggplot2::element_blank())
7.7 Figure 5E: Co-localized spots for Epithelial cells
Visualize the spots that contain cell types co-localized with Epithelial cells:
#Epithelial
df=dat
df_new=df[df$Epithelial>0.25,]
df_new=df_new[df_new$Fibroblasts>0.25 | df_new$Myo.Meso>0.25 |
df_new$Endothelium>0.25 | df_new$Pericytes>0.25 | df_new$Neural>0.25 |
df_new$Immune>0.25 | df_new$Muscle>0.25,-c(1:3)]
df_new$CellType=NA
for(i in 1:nrow(df_new)){
df_new$CellType[i]=names(which.max(df_new[i,-c(1:2,4)]))
}
df_new$CellType=factor(df_new$CellType,c("Immune", "Myo.Meso",
"Muscle","Neural",
"Endothelium",
"Pericytes","Fibroblasts"))
ggplot2::ggplot(df_new, ggplot2::aes(x=imagerow, y=imagecol)) +
ggplot2::ylim(min(df$imagecol),max(df$imagecol)) +
ggplot2::xlim(min(df$imagerow),max(df$imagerow))+
ggplot2::geom_point(size=1.8, shape=21, ggplot2::aes(fill=CellType))+
ggplot2::scale_fill_manual(values=c("#E69F00", "#56B4E9", "#0072B2","#F0E442"),
labels=c("Immune", "Myofibroblasts\nMesothelium", "Endothelium",
"Fibroblasts"))+
ggplot2::xlab("") + ggplot2::ylab("") +
ggplot2::theme_classic()+
ggplot2::theme(legend.key.height = ggplot2::unit(0.2, 'cm'), #change legend key size
legend.key.width = ggplot2::unit(1, 'cm'),
legend.title = ggplot2::element_blank(),
legend.position = "bottom",
plot.margin = ggplot2::margin(-0.15, -0.5, 0.2, -0.55, "cm"), #A3
axis.line = ggplot2::element_blank(),
axis.text.x = ggplot2::element_blank(), axis.text.y = ggplot2::element_blank(),
axis.ticks.x=ggplot2::element_blank(),axis.ticks.y=ggplot2::element_blank())
7.8 Figure 6C: Concordance between expression profiles of found genes obtained from RETROFIT and scRNA-seq data
df=vignetteColonData$marker_ref_df
gene1=vignetteColonData$fetal12_genes
gene1=gene1[!(gene1 %in% df$Gene)] #common genes
W1=vignetteColonData$a3_results_4k_iterations$annotateWithCorrelations$w
W12=vignetteColonData$intestine_w_12pcw
W12=W12[gene1,]
W12_prop=W12
w_rowsums1 = rowSums(W12)
for (i in 1:length(w_rowsums1)){
if(w_rowsums1[i] > 0){
W12_prop[i,] = W12_prop[i,]/w_rowsums1[i]
}
}
W1_prop=W1[gene1,-c(1:2)]
dat=data.frame(gene=c(rep(gene1,8)),
celltype=factor(c(rep("Epithelial",length(gene1)),rep("Fibroblasts",length(gene1)),
rep("Myofibroblasts\nMesothelium",length(gene1)),rep("Endothelium",length(gene1)),
rep("Pericytes",length(gene1)),rep("Neural",length(gene1)),
rep("Immune",length(gene1)),rep("Muscle",length(gene1))
),levels=c("Epithelial","Immune","Fibroblasts","Endothelium",
"Neural","Pericytes", "Myofibroblasts\nMesothelium","Muscle")),
stage=c(rep("Fetal 12 PCW (B)",length(gene1)*8)),
gene_exp1=c(W1_prop[gene1,"Epithelial"],W1_prop[gene1,"Fibroblasts"],
W1_prop[gene1,"Myo.Meso"],W1_prop[gene1,"Endothelium"],
W1_prop[gene1,"Pericytes"],W1_prop[gene1,"Neural"],
W1_prop[gene1,"Immune"],W1_prop[gene1,"Muscle"]
),
gene_exp2=c(W12_prop[gene1,"Epithelial"],W12_prop[gene1,"Fibroblasts"],
W12_prop[gene1,"Myo.Meso"],W12_prop[gene1,"Endothelium"],
W12_prop[gene1,"Pericytes"],W12_prop[gene1,"Neural"],
W12_prop[gene1,"Immune"],W12_prop[gene1,"Muscle"]
))
ggplot2::ggplot(dat, ggplot2::aes(celltype, gene)) +
ggplot2::geom_point(shape=21, ggplot2::aes(fill=gene_exp1, size=gene_exp2)) +
ggplot2::theme_classic() +
ggplot2::scale_fill_gradientn(colors = pals::brewer.blues(20)[2:20],
name = "Expression (RETROFIT)") +
ggplot2::facet_grid(cols=ggplot2::vars(stage))+
ggplot2::theme(axis.text.x=ggplot2::element_text(size=20, angle = 45, hjust = 1),
axis.text.y=ggplot2::element_text(size=20),
legend.title=ggplot2::element_text(size=20),
legend.text=ggplot2::element_text(size=20),
legend.key.width=ggplot2::unit(0.3,"cm"),
legend.position="right"
) +
ggplot2::guides(size=ggplot2::guide_legend("Expression (scRNA-seq)"))+
ggplot2::xlab('')+
ggplot2::ylab('Genes')+
ggplot2::theme()
8 Session information
sessionInfo()## R Under development (unstable) (2024-10-21 r87258)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] retrofit_1.7.0 Rcpp_1.0.13 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.9 utf8_1.2.4 generics_0.1.3
## [4] bitops_1.0-9 stringi_1.8.4 digest_0.6.37
## [7] magrittr_2.0.3 evaluate_1.0.1 grid_4.5.0
## [10] bookdown_0.41 maps_3.4.2 fastmap_1.2.0
## [13] plyr_1.8.9 jsonlite_1.8.9 pals_1.9
## [16] tinytex_0.53 BiocManager_1.30.25 fansi_1.0.6
## [19] scales_1.3.0 jquerylib_0.1.4 cli_3.6.3
## [22] rlang_1.1.4 munsell_0.5.1 withr_3.0.2
## [25] cachem_1.1.0 yaml_2.3.10 corrplot_0.95
## [28] tools_4.5.0 reshape2_1.4.4 dplyr_1.1.4
## [31] colorspace_2.1-1 ggplot2_3.5.1 mapproj_1.2.11
## [34] vctrs_0.6.5 R6_2.5.1 png_0.1-8
## [37] lifecycle_1.0.4 magick_2.8.5 stringr_1.5.1
## [40] pkgconfig_2.0.3 pillar_1.9.0 bslib_0.8.0
## [43] gtable_0.3.6 glue_1.8.0 xfun_0.48
## [46] tibble_3.2.1 tidyselect_1.2.1 highr_0.11
## [49] dichromat_2.0-0.1 knitr_1.48 farver_2.1.2
## [52] htmltools_0.5.8.1 rmarkdown_2.28 labeling_0.4.3
## [55] compiler_4.5.0 RCurl_1.98-1.16