Plot Soft Power Threshold results
Usage
PlotSoftPowers(
seurat_obj,
selected_power = NULL,
point_size = 5,
text_size = 3,
plot_connectivity = TRUE,
wgcna_name = NULL
)Arguments
- seurat_obj
A Seurat object
- selected_power
power to highlight in the plots
- point_size
the size of the points in the plot
- text_size
the size of the text in the plot
- plot_connectivity
logical indicating whether to plot the connectivity in addition to the scale free topplogy fit.
- wgcna_name
The name of the WGCNA experiment in seurat_obj
Examples
PlotSoftPowers
#> function (seurat_obj, selected_power = NULL, point_size = 5,
#> text_size = 3, plot_connectivity = TRUE, wgcna_name = NULL)
#> {
#> if (is.null(wgcna_name)) {
#> wgcna_name <- seurat_obj@misc$active_wgcna
#> }
#> pt <- GetPowerTable(seurat_obj, wgcna_name)
#> if ("group" %in% colnames(pt)) {
#> print("here")
#> power_tables <- pt %>% dplyr::group_split(group)
#> soft_powers <- sapply(power_tables, function(power_table) {
#> power_table %>% subset(SFT.R.sq >= 0.8) %>% .$Power %>%
#> min
#> })
#> }
#> else {
#> if (is.null(selected_power)) {
#> soft_power <- pt %>% subset(SFT.R.sq >= 0.8) %>%
#> .$Power %>% min
#> }
#> else {
#> soft_power <- selected_power
#> }
#> soft_powers <- NULL
#> power_tables <- list(power = pt)
#> }
#> plot_list <- list()
#> for (i in 1:length(power_tables)) {
#> pt <- power_tables[[i]]
#> if (!is.null(soft_powers)) {
#> soft_power <- soft_powers[i]
#> print(i)
#> print(soft_power)
#> pt <- pt %>% dplyr::select(-group)
#> }
#> print(head(pt))
#> sft_r <- as.numeric(pt[pt$Power == soft_power, "SFT.R.sq"])
#> mean_k <- as.numeric(pt[pt$Power == soft_power, "mean.k."])
#> median_k <- as.numeric(pt[pt$Power == soft_power, "median.k."])
#> max_k <- as.numeric(pt[pt$Power == soft_power, "max.k."])
#> pt$text_color <- ifelse(pt$Power == soft_power, "white",
#> "black")
#> p1 <- pt %>% ggplot(aes(x = Power, y = SFT.R.sq)) + geom_rect(data = pt[1,
#> ], aes(xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = 0.8),
#> fill = "grey80", alpha = 0.8, color = NA) + geom_hline(yintercept = sft_r,
#> linetype = "dashed") + geom_vline(xintercept = soft_power,
#> linetype = "dashed") + geom_point(data = pt[pt$Power ==
#> soft_power, c("Power", "SFT.R.sq")], aes(x = Power,
#> y = SFT.R.sq), inherit.aes = FALSE, color = "black",
#> size = point_size) + geom_text(label = pt$Power,
#> color = pt$text_color, size = text_size) + scale_y_continuous(limits = c(0,
#> 1), breaks = c(0, 0.2, 0.4, 0.6, 0.8, 1)) + ylab("Scale-free Topology Model Fit") +
#> xlab("Soft Power Threshold") + theme(axis.line.x = element_blank(),
#> axis.line.y = element_blank(), panel.border = element_rect(colour = "black",
#> fill = NA, size = 1))
#> if (plot_connectivity) {
#> p2 <- pt %>% ggplot(aes(x = Power, y = mean.k.)) +
#> geom_hline(yintercept = mean_k, linetype = "dashed") +
#> geom_vline(xintercept = soft_power, linetype = "dashed") +
#> geom_point(data = pt[pt$Power == soft_power,
#> c("Power", "mean.k.")], aes(x = Power, y = mean.k.),
#> inherit.aes = FALSE, color = "black", size = point_size) +
#> geom_text(label = pt$Power, color = pt$text_color,
#> size = text_size) + scale_y_continuous(labels = scales::comma) +
#> ylab("Mean Connectivity") + xlab("Soft Power Threshold") +
#> theme(axis.line.x = element_blank(), axis.line.y = element_blank(),
#> panel.border = element_rect(colour = "black",
#> fill = NA, size = 1))
#> p3 <- pt %>% ggplot(aes(x = Power, y = median.k.)) +
#> geom_hline(yintercept = median_k, linetype = "dashed") +
#> geom_vline(xintercept = soft_power, linetype = "dashed") +
#> geom_point(data = pt[pt$Power == soft_power,
#> c("Power", "median.k.")], aes(x = Power, y = median.k.),
#> inherit.aes = FALSE, color = "black", size = point_size) +
#> geom_text(label = pt$Power, color = pt$text_color,
#> size = text_size) + scale_y_continuous(labels = scales::comma) +
#> ylab("Median Connectivity") + xlab("Soft Power Threshold") +
#> theme(axis.line.x = element_blank(), axis.line.y = element_blank(),
#> panel.border = element_rect(colour = "black",
#> fill = NA, size = 1))
#> p4 <- pt %>% ggplot(aes(x = Power, y = max.k.)) +
#> geom_hline(yintercept = max_k, linetype = "dashed") +
#> geom_vline(xintercept = soft_power, linetype = "dashed") +
#> geom_point(data = pt[pt$Power == soft_power,
#> c("Power", "max.k.")], aes(x = Power, y = max.k.),
#> inherit.aes = FALSE, color = "black", size = point_size) +
#> geom_text(label = pt$Power, color = pt$text_color,
#> size = text_size) + scale_y_continuous(labels = scales::comma) +
#> ylab("Max Connectivity") + xlab("Soft Power Threshold") +
#> theme(axis.line.x = element_blank(), axis.line.y = element_blank(),
#> panel.border = element_rect(colour = "black",
#> fill = NA, size = 1))
#> plot_list[[i]] <- list(p1, p2, p3, p4)
#> }
#> else {
#> plot_list[[i]] <- p1
#> }
#> }
#> if (length(plot_list) == 1) {
#> return(plot_list[[1]])
#> }
#> plot_list
#> }
#> <bytecode: 0x7f963b5f7e80>
#> <environment: namespace:hdWGCNA>