Unable to open pdf file of volcano plots created using many group comparisons from EnhancedVolcano package in R

Question

[mohammedtoufiq91]

Hi,

I am working with a dataframe in R containing the quantitative data and trying to plot a volcano plot using library(EnhancedVolcano) package. I am currently analyzing by subsetting based on corresponding matching pairs of "Coef" and "P.value" obtained from limma (for instance; Coef.HC_6h_vs_0h and P.value.HC_6h_vs_0h) individually and export the pdf plot. I have many matching paired columns, this process becomes very tedious and cumbersome. I took some help to create a forloop on each matching pairs of "Coef" and "P.value" to generate separate plots in the form of the pdf file. The exported pdf files exists but it cannot be opened. I have provided the example below. Please advise on how to solve this.

library(tidyverse)
library(EnhancedVolcano)
DF <- structure(list(Coef.HC_6h_vs_0h = c(NA, NA, 0.048151066, 1.130642422, 
                                          0.68074318, 0.063779224, -0.358027426, -0.241326901, 0.167703878, 
                                          -0.257097748, -2.327977345, 1.300506434, 0.037118733, 0.036362435, 
                                          0.018953335, -0.215582086, -0.215130266, -1.642467234, 0.225615042, 
                                          0.212244164), 
                     Coef.HC_LTA_vs_6h = c(NA, NA, NA, 0.571320992, 
                                           0.240900855, 0.664981117, -0.080211466, 0.007521568, 0.032402696, 
                                           0.369452449, 0.934659157, 1.861006387, -0.338416494, 0.127921196, 
                                           0.040630241, 0.275547134, 0.952987298, 0.433537994, 0.492574777, 
                                           -0.099178916), 
                     Coef.UC_Rem_LPS_vs_6h = c(-0.259935478, -0.105746142, 
                                               0.207159012, 1.147068093, 0.211020926, 0.532359869, -0.101653129, 
                                               0.20209878, 0.016125514, 1.32593494, 1.496175233, 2.104156173, 
                                               -0.667087007, 0.154297917, 0.272351994, 0.791148254, 0.35998438, 
                                               1.399002196, 0.196009571, 0.619367312), 
                     Coef.CD_Mil_FLA_vs_6h = c(0.261472621, 
                                               -0.25263016, -0.041481308, -0.096265831, 0.004722895, 0.084040658, 
                                               -0.048078762, 0.009246748, -0.234490949, 0.273803791, 1.480274922, 
                                               0.292870886, -0.143628372, 0.087706716, -0.002301245, 0.15003941, 
                                               -0.314001872, 0.24746456, 0.617210833, -0.018220783), 
                     P.value.HC_6h_vs_0h = c(0.545376281, 
                                             0.011772197, 0.821228333, 6.67e-05, 0.415510885, 0.796781833, 
                                             0.136254462, 0.313415856, 0.589642204, 0.337351766, 0.023366465, 
                                             0.017807501, 0.860263888, 0.882854509, 0.956424822, 0.299125336, 
                                             0.622690737, 2.11e-06, 0.691578797, 0.474612129), 
                     P.value.HC_LTA_vs_6h = c(0.863203348, 
                                              0.465183842, 0.064113571, 0.043226481, 0.768757045, 0.00736856, 
                                              0.738392724, 0.97492814, 0.916995649, 0.168106123, 0.249987701, 
                                              0.000163064, 0.108745568, 0.598176335, 0.906755014, 0.184550004, 
                                              0.026536555, 0.208004113, 0.386500216, 0.73827056), 
                     P.value.UC_Rem_LPS_vs_6h = c(0.580841515, 
                                                  0.728198309, 0.331085948, 5.23e-05, 0.796764557, 0.031810205, 
                                                  0.672110689, 0.398510201, 0.958635746, 8.81e-07, 0.107068282, 
                                                  1.5e-05, 0.001603959, 0.52498963, 0.432437774, 0.000146689, 0.410210239, 
                                                  5.2e-05, 0.73035002, 0.037133718), 
                     P.value.CD_Mil_FLA_vs_6h = c(0.564348495, 
                                                  0.406476956, 0.845654459, 0.733110608, 0.995400367, 0.73437091, 
                                                  0.841329565, 0.969180147, 0.450794691, 0.306914258, 0.148066231, 
                                                  0.558742168, 0.49581594, 0.717831127, 0.994706662, 0.469835936, 
                                                  0.456921237, 0.47220793, 0.277934735, 0.951048936)), 
                class = "data.frame", row.names = c("Gene_1","Gene_2", "Gene_3", "Gene_4", "Gene_5", "Gene_6", "Gene_7", "Gene_8", 
                                                    "Gene_9", "Gene_10", "Gene_11", "Gene_12", "Gene_13", "Gene_14", 
                                                    "Gene_15", "Gene_16", "Gene_17", "Gene_18", "Gene_19", "Gene_20"))


DFlong <- DF %>% rownames_to_column() %>%  pivot_longer(cols = -rowname, names_pattern = "(Coef|P.value)\\.(.+)",
                                                        names_to = c(".value","Case"))

Cases <- unique(DFlong$Case)
for (Case in Cases) {
  Data <- filter(DFlong, Case == Case)
  pdf(paste0("Plot_for_", Case, ".pdf"), height = 7, width = 7)
  EnhancedVolcano(Data,
                  lab = Data$rowname,
                  x = 'Coef',
                  y = 'P.value',
                  title = Case,
                  pCutoff = 0.05,
                  FCcutoff = 1.0,
                  pointSize = 3.0,
                  labSize = 6.0)
  dev.off()
}

Thank you,

Toufiq

Answer 1

[ATpoint]

It's ggplot so you have to wrap the actual plot command into print(), so print(EnhancedWhatever(...))

https://www.datanovia.com/en/blog/how-to-save-a-ggplot/

[Ram]

Or use ggsave() instead of pdf(); print(); dev.off() - it's neater.

plotObj <- EnhancedVolcano(...)
ggsave(plotObj, pdf_file, ...)

[mohammedtoufiq91]

Ram thank you fo the suggestion. This was helpful as well.

[mohammedtoufiq91]

ATpoint, thank you. This fixed my query.