Loop through a list of dataframes output plots - r

Question

I try to make function plots or my top 20 genes. That's why I created a list of data frames, these data frames exist or different columns contain values ​​and names.
One of these columns in the data frame is the gene column. My code turns the first 20 genes into function plots. But now I have the problem in some of the data frames that exist
fewer than 20 genes. This causes my code to abort.
Because I want a maximum of 5 function plots per page, I cannot just define a counter.
Thank you for the input.
Example of my list or data frames
listGroups
group1_2: 'data.frame': 68 obs. of 7 variables:
..$ p_val: num [1:68] 1.15 1.43 ...
..$ score: num [1:68] 15.5 27.14 ...
..$ gene: Factor w/ 68 levels "BRA1", "NED",...: 41 52 ...
group2_3: 'data.frame': 3 obs. of 7 variables:
..$ p_val: num [1:3] 1.15 1.43 ...
..$ score: num [1:3] 15.5 27.14 ...
..$ gene: Factor w/ 3 levels "BCL12", "DEF1",...: 41 52 ...
Code
groupNames <- c("cluster1_2","cluster2_3","cluster3_4","cluster4_5","cluster5_6")
for (i in 1:length(listGroups)) {
Grouplist <- listGroups[[i]]
genesList <- Grouplist['gene']
lengths(geneList)
print(groupNames[i])
# Make Featureplots for top20 DE genes per cluster_group
pdf(file=paste0(sampleFolder,"/Featureplots_cluster_",groupNames[i],"_",sampleName,".pdf"))
print(FeaturePlot(object = seuratObj, features = c(as.character(genesList[1:5,]))))
print(FeaturePlot(object = seuratObj, features = c(as.character(genesList[6:10,]))))
print(FeaturePlot(object = seuratObj, features = c(as.character(genesList[11:15,]))))
print(FeaturePlot(object = seuratObj, features = c(as.character(genesList[16:20,]))))
dev.off()
}

Answer 1

For each genelist you could make one plot with your choice of genes like this (plot would look fine with larger size, as in your PDF):
use combine=FALSE and limit the number of features to plot to something like rownames(pbmc_small)[1 : min(20, nrow(pbmc_small))] to avoid errors
then export the list of single plots (allows for themeing) and plot into pdf using cowplot::plot_grid
instead of plotting within the function (plot(out)), you could export to pdf (maybe pass filename as second argument to function).
library(Seurat)
genelist <- list(
l1 = sample(rownames(pbmc_small), 23),
l2 = sample(rownames(pbmc_small), 14),
l3 = sample(rownames(pbmc_small), 4))
plotFeatures <- function(x){
p <- FeaturePlot(object = pbmc_small,
features = x[1 : min(20, length(x))],
combine = FALSE, label.size = 2)
out <- cowplot::plot_grid(plotlist = p, ncol = 5, nrow = 4)
plot(out)
}
lapply(genelist, plotFeatures)

Answer 2

Not tested, something like this should work. Instead of calling print 5 times for each 5 genes, we call it in a loop n times based on number of genes. If we have 10 genes forloop will print twice, if 20 then we call print 4 times, etc:
groupNames <- c("cluster1_2","cluster2_3","cluster3_4","cluster4_5","cluster5_6")
for (i in 1:length(listGroups)) {
Grouplist <- listGroups[[i]]
genesList <- Grouplist['gene']
#lengths(geneList)
print(groupNames[i])
# Make Featureplots for top20 DE genes per cluster_group
# make chunks of 5 each.
myChunks <- split(genesList, ceiling(seq_along(genesList)/5))
pdf(file=paste0(sampleFolder,"/Featureplots_cluster_",groupNames[i],"_",sampleName,".pdf"))
# loop through genes plotting 5 genes each time.
for(x %in% seq(myChunks) ){
print(FeaturePlot(object = seuratObj, features = myChunks[[ x ]]))
}
dev.off()
}

Answer 3

Thanks to the input of zx8754 and user12728748. I found two solutions for my problem.
for (i in 1:length(listGroups)) {
Grouplist <- listGroups[[1]]
genesList <- Grouplist['gene']
print(groupNames[1])
## Solution 1
# Here all genes are printed. I didn't find a way yet to limited to 20
# make chunks of 5 each.
myChunks <- split(genesList,ceiling(seq(lengths(genesList))/5))
# Make Featureplots for top20 DE genes per cluster_group
pdf(file=paste0(sampleFolderAggr,"results/Featureplots_",groupNames[i],"_",sampleNameAggr,".pdf"))
# loop through genes plotting 5 genes each time.
for(x in 1:min(5, length(myChunks) ){
# Create a list of 5 genes
my5Genes <- as.list(myChunks[[x]])
print(FeaturePlot(object = seuratObj, features = c(as.character(my5Genes$gene))))
}
dev.off()
## Solution 2
pdf(file=paste0(sampleFolderAggr,"results/Featureplots_",groupNames[i],"_",sampleNameAggr,".pdf"))
plotFeatures <- function(x){
p <- FeaturePlot(object = seuratObj, features = c(as.character(x[1: min(20, lengths(x)),])), combine = FALSE, label.size = 2)
out <- cowplot::plot_grid(plotlist = p, ncol = 5, nrow = 4)
# Make Featureplots for top20 DE genes per cluster_group
plot(out)
}
lapply(genelist, plotFeatures)
dev.off()
}