For making a scatterplot of a flow cytometry experiment, I used the following code for the last few weeks. While running the code, I did not receive a significant amount of errors (only 20 out of 10,000 entries were removed from the dataset).
visual <- ggplot(data=dots, aes(GRNHLin, REDHLin)) +
geom_point(colour=rgb(0.17, 0.44, 0.71), size=0.500, alpha=0.250) +
#stat_density_2d(aes(alpha = ..density..), geom = 'tile', contour = FALSE) +
geom_tile(aes(width = 0.004)) +
scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x)), limits = c(1,1e4)) +
scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x)), limits = c(1,1e3)) +
geom_vline(xintercept=threshold_green) +
labs(x="Green Fluorescence Intensity", y="Red Fluorescence Intensity", size=18)
visual
Now that I want to use model-based clustering from the Mclust-package, I use fviz_cluster as a function to create a scatterplot. Only this time, I receive the following error after running the code below.
Warning messages: 1: In self$trans$transform(x) : NaNs produced 2: Transformation introduced infinite values in continuous x-axis 3: In self$trans$transform(x) : NaNs produced 4: Transformation introduced infinite values in continuous y-axis 5: Removed 9110 rows containing missing values (geom_point).
dots <- read_csv(file_of_sample)
names(dots) <- str_replace_all(names(dots), c("-" = ""))
dots <- dots %>%
select("GRNHLin", "RED2HLin")
dots <- dots %>%
filter(RED2HLin >= 1.0)
dots.Mclust <- Mclust(dots, modelNames="VVV", G=8)
#BIC <- mclustBIC(logdots)
#ICL <- mclustICL(logdots)
#summary(BIC)
#summary(ICL)
visual <- fviz_cluster(dots.Mclust,
ellipse=FALSE,
shape=20,
ellipse.alpha = 0.1,
alpha=0.450,
geom = c("point"),
show.clust.cent = FALSE,
main = FALSE,
legend = c("right"),
palette = "npg",
legend.title = "Clusters"
) +
labs(x="Green Fluorescence Intensity", y="Red Fluorescence Intensity") +
scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x)), limits = c(1,1e4)) +
scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x)), limits = c(1,1e3))
visual
Can anyone help me out with this issue?