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‎DESCRIPTION

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@@ -2,8 +2,8 @@ Package: espresso
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Type: Package
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Title: Enhanced spatial reconstruction by stochastic self-organizing
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map
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Version: 1.0.0
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Date: 2022-01-21
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Version: 1.0.1
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Date: 2022-03-04
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Authors@R: person("Tomoya", "Mori", role = c("aut", "cre"), email = "[email protected]")
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Description: This is a package for domain estimation of cells only from gene expression profile based on graph-structured stochastic self-organizing map (GraphSOM) and Markov chain Monte Carlo (MCMC) method.
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License: GPL-3
@@ -18,6 +18,6 @@ LazyData: true
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Suggests: knitr, rmarkdown
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VignetteBuilder: knitr
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NeedsCompilation: no
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Packaged: 2022-01-21 06:50:12 UTC; tmori
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Packaged: 2022-03-31 07:45:12 UTC; tmori
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Author: Tomoya Mori [aut, cre]
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Maintainer: Tomoya Mori <[email protected]>

‎NAMESPACE

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@@ -18,6 +18,7 @@ import(Boruta)
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import(RColorBrewer)
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import(doParallel)
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import(foreach)
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import(grid)
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import(parallel)
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import(progress)
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import(rFerns)

‎NEWS.md

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## 1.0.1
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* Modify the argument name from `version="0.2.17` to `version="0"` to run SOM in the previous version.
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* Default output format of `plotUMAP` is changed from "pdf" to "png".
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* Modify labels of legend in distance map to discrete ones.
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## 1.0.0
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* Add an option `version` to `graphSOM` and `rxmcmc` functions in order to enable us to perform SOM computations based on the previous version (= 0.2.17).
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‎R/distancemap.R

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@@ -10,6 +10,7 @@
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#' @importFrom pheatmap pheatmap
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#' @importFrom grDevices colorRampPalette
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#' @import RColorBrewer
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#' @import grid unit
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#' @export
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#'
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plotDistMap <- function(obj, type = "b", size_d = NULL, size_s = 5) {
@@ -22,16 +23,27 @@ plotDistMap <- function(obj, type = "b", size_d = NULL, size_s = 5) {
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# Plot distance maps of domains before GraphSOM ------------------------
2425
if (!is.null(size_d)) {
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pheatmap(distmat, cluster_cols = F, cluster_rows = F,
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color = colorRampPalette(brewer.pal(n = 7, name = "Blues"))(100), na_col = "black",
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main = "Distance of domains",
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fontsize_row = size_d, fontsize_col = size_d,
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cellheight = size_d, cellwidth = size_d
30-
)
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p <- pheatmap(distmat, cluster_cols = F, cluster_rows = F,
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color = colorRampPalette(brewer.pal(n = 7, name = "Blues"))(max(eobj@dist[eobj@dist != Inf]) + 1), na_col = "black",
28+
main = "Distance of domains",
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fontsize_row = size_d, fontsize_col = size_d,
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cellheight = size_d, cellwidth = size_d, silent = T,
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legend_breaks = 0:max(eobj@dist[eobj@dist != Inf]),
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legend_labels = 0:max(eobj@dist[eobj@dist != Inf])
33+
)
34+
p <- .modLabelPositions(p)
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plot.new()
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print(p)
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} else {
32-
pheatmap(distmat, cluster_cols = F, cluster_rows = F,
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color = colorRampPalette(brewer.pal(n = 7, name = "Blues"))(100), na_col = "black",
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main = "Distance of domains")
38+
p <- pheatmap(distmat, cluster_cols = F, cluster_rows = F,
39+
color = colorRampPalette(brewer.pal(n = 7, name = "Blues"))(max(eobj@dist[eobj@dist != Inf]) + 1), na_col = "black",
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main = "Distance of domains", silent = T,
41+
legend_breaks = 0:max(eobj@dist[eobj@dist != Inf]),
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legend_labels = 0:max(eobj@dist[eobj@dist != Inf])
43+
)
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p <- .modLabelPositions(p)
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plot.new()
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print(p)
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}
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}
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if (type == "s" || type == "b") {
@@ -55,13 +67,19 @@ plotDistMap <- function(obj, type = "b", size_d = NULL, size_s = 5) {
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} else {
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main_title <- paste("Distance of sample cells\n(rept.", i, ")", sep ="")
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}
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pheatmap(sample_dist,
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cluster_cols = F, cluster_rows = F,
60-
fontsize_row = size_s, fontsize_col = size_s,
61-
cellheight = size_s, cellwidth = size_s,
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color = colorRampPalette(brewer.pal(n = 7, name = "Blues"))(100), na_col = "black",
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main = main_title
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p <- pheatmap(sample_dist,
71+
cluster_cols = F, cluster_rows = F,
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fontsize_row = size_s, fontsize_col = size_s,
73+
cellheight = size_s, cellwidth = size_s,
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color = colorRampPalette(brewer.pal(n = 7, name = "Blues"))(max(eobj@dist[eobj@dist != Inf]) + 1), na_col = "black",
75+
main = main_title, silent = T,
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legend_breaks = 0:max(eobj@dist[eobj@dist != Inf]),
77+
legend_labels = 0:max(eobj@dist[eobj@dist != Inf])
6478
)
79+
p <- .modLabelPositions(p)
80+
plot.new()
81+
print(p)
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for (repl in names(obj@bmu)) {
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# Plot distance maps of samples after GraphSOM -------------------------
6785
if (!is.null(obj@bmu)) {
@@ -97,13 +115,18 @@ plotDistMap <- function(obj, type = "b", size_d = NULL, size_s = 5) {
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}
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vec <- as.vector(sample_dist2)
99117
if (length(unique(vec[!is.na(vec)])) != 1) {
100-
pheatmap(sample_dist2,
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cluster_cols = F, cluster_rows = F,
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fontsize_row = size_s, fontsize_col = size_s,
103-
cellheight = size_s, cellwidth = size_s,
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color = colorRampPalette(brewer.pal(n = 7, name = "Blues"))(100), na_col = "black",
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main = main_title
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p <- pheatmap(sample_dist2,
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cluster_cols = F, cluster_rows = F,
120+
fontsize_row = size_s, fontsize_col = size_s,
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cellheight = size_s, cellwidth = size_s,
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color = colorRampPalette(brewer.pal(n = 7, name = "Blues"))(max(eobj@dist[eobj@dist != Inf]) + 1), na_col = "black",
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main = main_title, silent = T,
124+
legend_breaks = 0:max(eobj@dist[eobj@dist != Inf]),
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legend_labels = 0:max(eobj@dist[eobj@dist != Inf])
106126
)
127+
p <- .modLabelPositions(p)
128+
plot.new()
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print(p)
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# Plot distance maps of samples before/after GraphSOM -------------------
108131
ds <- sample_dist
109132
ds[upper.tri(ds)] <- sample_dist2[upper.tri(sample_dist2)]
@@ -124,13 +147,18 @@ plotDistMap <- function(obj, type = "b", size_d = NULL, size_s = 5) {
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main_title <- paste("Distance of sample cells \nin original (lower) and after GraphSOM (upper)\n(rept.", i, ")", sep = "")
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}
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}
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pheatmap(ds,
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cluster_cols = F, cluster_rows = F,
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fontsize_row = size_s, fontsize_col = size_s,
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cellheight = size_s, cellwidth = size_s,
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color = colorRampPalette(brewer.pal(n = 7, name = "Blues"))(100), na_col = "black",
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main = main_title
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p <- pheatmap(ds,
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cluster_cols = F, cluster_rows = F,
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fontsize_row = size_s, fontsize_col = size_s,
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cellheight = size_s, cellwidth = size_s,
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color = colorRampPalette(brewer.pal(n = 7, name = "Blues"))(max(eobj@dist[eobj@dist != Inf]) + 1), na_col = "black",
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main = main_title, silent = T,
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legend_breaks = 0:max(eobj@dist[eobj@dist != Inf]),
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legend_labels = 0:max(eobj@dist[eobj@dist != Inf])
133158
)
159+
p <- .modLabelPositions(p)
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plot.new()
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print(p)
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} else {
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warning("Distance map after graph-SOM clustering cannot be drown since only one cluseter was generated.")
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}
@@ -139,4 +167,29 @@ plotDistMap <- function(obj, type = "b", size_d = NULL, size_s = 5) {
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}
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}
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}
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}
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# =============================================================================
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#' @title Modify label positions.
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#' @description This function modifies positions of labels
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#' @param p \code{pheatmap} object.
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#' @importFrom pheatmap pheatmap
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#' @import grid unit
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#'
181+
.modLabelPositions <- function(p) {
182+
N_col_areas <- length(p$gtable$grobs[[5]]$children[[1]]$y)
183+
N_labels <- length(p$gtable$grobs[[5]]$children[[2]]$label)
184+
yseq1 <- seq(0, 1, length.out=N_col_areas)
185+
center <- yseq1[2]/2
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yseq2 <- seq(center, 1-center, length.out=N_labels)
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188+
for (k in 1:(N_labels)) {
189+
p$gtable$grobs[[5]]$children[[2]]$y[[k]] <-
190+
sum(yseq2[k]*min(unit(1,"npc"), unit(150,"bigpts")),
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unit(1,"npc"),
192+
-1*min(unit(1,"npc"), unit(150,"bigpts")))
193+
}
194+
return(p)
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}

‎R/graphsom.R

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@@ -607,7 +607,7 @@ initGraphSOM <- function(obj, nsamples = NULL, rept = 1,
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#' @param gset Gene set.
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#' @param seed Random seed.
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#' @param verbose Whether to show messages.
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#' @param version Character that specifies on which previous version GraphSOM computation should be performed. (e.g., "0.2.17")
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#' @param version Character that specifies on which previous version GraphSOM computation should be performed. (e.g., "0")
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#' @return \code{espresso} object
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#' @export
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#'
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if (!is.null(seed)) {
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set.seed(seed, kind = "L'Ecuyer-CMRG")
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}
619-
} else if (version == "0.2.17") {
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} else if (version == "0") {
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if (!is.null(seed)) {
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set.seed(seed, kind = "Mersenne-Twister")
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}

‎R/rxmcmc.R

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#' @param n_repl Number of replicas (default: \code{detectCores()}).
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#' @param n_ig Number of initial genes randomly selected for MCMC.
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#' @param fact Scaling factor for computing selection probability.
210-
#' @param version Character that specifies on which previous version GraphSOM computation should be performed. (e.g., "0.2.17")
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#' @param version Character that specifies on which previous version GraphSOM computation should be performed. (e.g., "0")
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#' @import doParallel
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#' @import parallel
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#' @import foreach
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226226
warning("Input `gset` to be optimized.")
227227
return(obj)
228228
}
229-
if (version != "0.2.17" && !is.null(version)) {
229+
if (version != "0" && !is.null(version)) {
230230
stop(paste("version", version, "is not available."))
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return(obj)
232232
}
@@ -297,9 +297,9 @@ rxmcmc <- function(obj, gset = NULL, temp = 1.0, itr = 10, k = 1, seed = NULL,
297297
score_tmp[[l]] <- res_tmp@score
298298
summary_tmp[[l]] <- res_tmp@summary
299299
}
300-
} else if (version == "0.2.17"){
300+
} else if (version == "0"){
301301
for (l in 1:n_sets) {
302-
res_tmp <- graphSOM(obj, gset = cand_sets[[l]], verbose = FALSE, version = "0.2.17")
302+
res_tmp <- graphSOM(obj, gset = cand_sets[[l]], verbose = FALSE, version = "0")
303303
res[l, ] <- c(as.numeric(unlist(res_tmp@summary)), length(cand_sets[[l]]))
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map_tmp[[l]] <- res_tmp@map
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bmu_tmp[[l]] <- res_tmp@bmu

‎R/umap.R

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#' @importFrom scatterplot3d scatterplot3d
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#' @importFrom tagcloud smoothPalette
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#' @export
152-
plotUMAP <- function(obj, file = "umap.pdf",
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plotUMAP <- function(obj, file = "umap.png",
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movie = FALSE, dir = ".",
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mname = "movie",
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seed = 0,

‎README.md

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# eSPRESSO
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21-Jan-2022: espresso 1.0.0 released.
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31-Mar-2022: espresso 1.0.1 released.
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<br/>
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‎build/partial.rdb

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‎index.html

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‎inst/doc/espresso.R

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knitr::include_graphics("umap.all.png")
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## ---- eval = FALSE------------------------------------------------------------
279-
# graphSOM(eobj, gset = fgenes, seed = 0, version = "0.2.17")
279+
# graphSOM(eobj, gset = fgenes, seed = 0, version = "0")
280280

281281
## ---- eval = FALSE------------------------------------------------------------
282-
# rxmcmc(eobj, gset = fgenes, itr = 2, n_ex = 5, n_repl = 4, n_cl = 4, seed = 0, version = "0.2.17")
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# rxmcmc(eobj, gset = fgenes, itr = 2, n_ex = 5, n_repl = 4, n_cl = 4, seed = 0, version = "0")
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## ---- eval=FALSE--------------------------------------------------------------
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# library(biomaRt)

‎inst/doc/espresso.Rmd

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---
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title: "espresso"
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date: "21-Jan-2022: espresso 1.0.0 released."
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date: "31-Mar-2022: espresso 1.0.1 released."
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output:
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rmarkdown::html_vignette:
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toc: true
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__Note__
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615615
When the exported format is 'pdf' or 'eps', and `rgl = TRUE`,
616-
the legend information is not printed due to the design of `rgl` package.
616+
the legend information is not printed due to the design of `rgl` package.
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In addition, it often takes much time to draw UMAP plot as a PDF file when
618+
the number of samples is large. In such case, please output as a PNG file.
617619

618620

619621
### Other options of UMAP plotting
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707709
## Appendix
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709-
### Run `graphSOM` and `rxmcmc` of previous version (0.2.17)
710-
In `espresso` of version 0.2.17 or earlier, the reproducibility between the results of `graphSOM` and `rxmcmc` was not guaranteed, and a random number generation method different from version 1.0.0 or later was employed. The followings are examples of the way to run `graphSOM` and `rxmcmc` of version 0.2.17.
711+
### Run `graphSOM` and `rxmcmc` of previous version (0)
712+
In `espresso` of version 0, the reproducibility between the results of `graphSOM` and `rxmcmc` was not guaranteed, and a random number generation method different from version 1.0.0 or later was employed. The followings are examples of the way to run `graphSOM` and `rxmcmc` of version 0.
711713

712714
```{r, eval = FALSE}
713-
graphSOM(eobj, gset = fgenes, seed = 0, version = "0.2.17")
715+
graphSOM(eobj, gset = fgenes, seed = 0, version = "0")
714716
```
715717

716718
```{r, eval = FALSE}
717-
rxmcmc(eobj, gset = fgenes, itr = 2, n_ex = 5, n_repl = 4, n_cl = 4, seed = 0, version = "0.2.17")
719+
rxmcmc(eobj, gset = fgenes, itr = 2, n_ex = 5, n_repl = 4, n_cl = 4, seed = 0, version = "0")
718720
```
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### Get gene description via biomaRt

‎inst/doc/espresso.html

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‎man/dot-modLabelPositions.Rd

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‎man/graphSOM.Rd

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‎man/plotUMAP.Rd

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‎man/rxmcmc.Rd

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‎vignettes/espresso.Rmd

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---
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title: "espresso"
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date: "21-Jan-2022: espresso 1.0.0 released."
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date: "31-Mar-2022: espresso 1.0.1 released."
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output:
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rmarkdown::html_vignette:
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toc: true
@@ -613,7 +613,9 @@ dev.off()
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__Note__
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615615
When the exported format is 'pdf' or 'eps', and `rgl = TRUE`,
616-
the legend information is not printed due to the design of `rgl` package.
616+
the legend information is not printed due to the design of `rgl` package.
617+
In addition, it often takes much time to draw UMAP plot as a PDF file when
618+
the number of samples is large. In such case, please output as a PNG file.
617619

618620

619621
### Other options of UMAP plotting
@@ -706,15 +708,15 @@ knitr::include_graphics("umap.all.png")
706708

707709
## Appendix
708710

709-
### Run `graphSOM` and `rxmcmc` of previous version (0.2.17)
710-
In `espresso` of version 0.2.17 or earlier, the reproducibility between the results of `graphSOM` and `rxmcmc` was not guaranteed, and a random number generation method different from version 1.0.0 or later was employed. The followings are examples of the way to run `graphSOM` and `rxmcmc` of version 0.2.17.
711+
### Run `graphSOM` and `rxmcmc` of previous version (0)
712+
In `espresso` of version 0, the reproducibility between the results of `graphSOM` and `rxmcmc` was not guaranteed, and a random number generation method different from version 1.0.0 or later was employed. The followings are examples of the way to run `graphSOM` and `rxmcmc` of version 0.
711713

712714
```{r, eval = FALSE}
713-
graphSOM(eobj, gset = fgenes, seed = 0, version = "0.2.17")
715+
graphSOM(eobj, gset = fgenes, seed = 0, version = "0")
714716
```
715717

716718
```{r, eval = FALSE}
717-
rxmcmc(eobj, gset = fgenes, itr = 2, n_ex = 5, n_repl = 4, n_cl = 4, seed = 0, version = "0.2.17")
719+
rxmcmc(eobj, gset = fgenes, itr = 2, n_ex = 5, n_repl = 4, n_cl = 4, seed = 0, version = "0")
718720
```
719721

720722
### Get gene description via biomaRt

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