R code for bubbleplot

library(ggplot2)
library(dplyr)
library(readxl)

# Assuming you have already read the data with read_excel
mydat <- read_excel("Pathway_KEGG_1457_vs_mock_Top10.xlsx")

# Custom function to convert fraction to decimal
convert_fraction_to_decimal <- function(fraction) {
    parts <- strsplit(as.character(fraction), "/")[[1]]
    as.numeric(parts[1]) / as.numeric(parts[2])
}

mydat$GeneRatio <- sapply(mydat$Ratio, convert_fraction_to_decimal)
mydat$Description <- factor(mydat$Description, levels = unique(mydat$Description))
mydat$Category <- factor(mydat$Category, levels=c("Up-regulated","Down-regulated"))

description_order <- rev(c("TNF signaling pathway","Legionellosis","Cytokine-cytokine receptor interaction","Protein processing in endoplasmic reticulum","Toxoplasmosis","Fluid shear stress and atherosclerosis","Pathways in cancer","JAK-STAT signaling pathway","IL-17 signaling pathway","Influenza A","Transcriptional misregulation in cancer","Glycine serine and threonine metabolism","Antifolate resistance","Base excision repair","Metabolic pathways","Acute myeloid leukemia","Homologous recombination","Fanconi anemia pathway","Primary immunodeficiency","MAPK signaling pathway"))
mydat$Description <- factor(mydat$Description, levels = description_order)

# Set the size for axis labels larger than the axis text
axis_label_size <- 24

# Now, create the plot        
png("bubble_plot.png", width = 1000, height = 800)
ggplot(mydat, aes(x = GeneRatio, y = Description)) +
  geom_point(aes(color = Category, size = Count, alpha = abs(log10(FDR)))) +
  scale_color_manual(values = c("Up-regulated" = "red", "Down-regulated" = "blue")) +
  scale_size_continuous(range = c(4, 10)) +
  labs(x = "GeneRatio", y = "Pathway name", color="Category", size="Count", alpha="-log10(FDR)") +
  theme(
    axis.text.x = element_text(angle = 20, vjust = 0.5, size = 20),
    axis.text.y = element_text(size = 20),
    axis.title.x = element_text(size = axis_label_size),
    axis.title.y = element_text(size = axis_label_size),
    legend.text = element_text(size = 20),
    legend.title = element_text(size = 20),
    plot.title = element_text(size = axis_label_size)
  ) +
  guides(color = guide_legend(override.aes = list(size = 10)), alpha = guide_legend(override.aes = list(size = 10)))
dev.off()

R code for bubbleplot2

library(readxl)
library(ggplot2)
library(dplyr)
library(magrittr)
library(tidyr)
library(forcats)

# Read data from an Excel file
mydat <- read_excel("1457_M10_atlE_DEGs_all_pathway-2.xlsx")

mydat$Comparison <- factor(mydat$Comparison, levels=c("1457","1457-M10","1457∆atlE"))

description_order <- rev(c("Protein processing in endoplasmic reticulum","TNF signaling pathway","Legionellosis","Epstein-Barr virus infection","Toxoplasmosis","Osteoclast differentiation","Proteasome","Influenza A","Herpes simplex infection","HIF-1 signaling pathway","NOD-like receptor signaling pathway","Apoptosis","C-type lectin receptor signaling pathway","MAPK signaling pathway","Endocytosis","Neurotrophin signaling pathway","Ubiquitin mediated proteolysis","Pancreatic cancer"))
mydat$Description <- factor(mydat$Description, levels = description_order)

png("bubble_plot2.png", 1000, 800)
ggplot(mydat, aes(y = Description, x = Comparison)) +
  geom_point(aes(color = p.adjust), size = 10) + # Set fixed size for points
  labs(x = "", y = "", alpha="-log10(p.adjust)") +
  theme(axis.text.x = element_text(angle = 20, vjust = 0.5)) +
  theme(axis.text = element_text(size = 20)) +
  theme(legend.text = element_text(size = 20)) +
  theme(legend.title = element_text(size = 20)) +
  guides(size = "none") # Turn off size in legend
dev.off()

Input Excel for bubbleplot

Description Size    Expect  Ratio   P Value FDR Category    Count
TNF signaling pathway   110 93/373  42/839  2.22E-12    7.24E-10    Up-regulated    42
Legionellosis   55  46/686  55/691  2.9E-10 4.72E-08    Up-regulated    55
Cytokine-cytokine receptor interaction  294 24/956  26/046  1.95E-09    2.12E-07    Up-regulated    26
Protein processing in endoplasmic reticulum 165 14/006  30/701  1.01E-07    8.27E-06    Up-regulated    30
Toxoplasmosis   113 95/919  35/447  2.2E-07 1.43E-05    Up-regulated    35
Fluid shear stress and atherosclerosis  139 11/799  31/359  1.52E-06    8.26E-05    Up-regulated    31
Pathways in cancer  526 44/649  19/037  1.92E-05    0.000896    Up-regualted    19
JAK-STAT signaling pathway  162 13/751  27/634  4.35E-05    0.00177 Up-regulated    27
IL-17 signaling pathway 93  78/942  32/935  0.000285    1.0327E-06  Up-regulated    32
Influenza A 171 14/515  25/491  0.000687    2.241E-06   Up-regulated    25
Transcriptional misregulation in cancer 186 83/425  23/974  0.0002368   0.038559    Down-regulated  23
Glycine serine and threonine metabolism 40  17/941  44/591  0.00032864  0.038559    Down-regulated  44
Antifolate resistance   31  13/904  50/345  0.00035484  0.038559    Down-regulated  50
Base excision repair    33  14/801  47/294  0.00053358  0.043487    Down-regulated  47
Metabolic pathways  1305    58/532  12/984  0.0075183   0.40292 Down-regulated  12
Acute myeloid leukemia  66  29/602  27/025  0.008932    0.40292 Down-regulated  27
Homologous recombination    41  18/389  32/628  0.0092737   0.40292 Down-regulated  32
Fanconi anemia pathway  54  24/220  28/902  0.0098875   0.40292 Down-regulated  28
Primary immunodeficiency    37  16/595  30/129  0.023604    0.77755 Down-regulated  30
MAPK signaling pathway  295 13/231  15/871  0.023851    0.77755 Down-regulated  15

Input Excel for bubbleplot2

Comparison  Description p.adjust
1457    Protein processing in endoplasmic reticulum 6.7681E-08
1457-M10    Protein processing in endoplasmic reticulum 4.6253E-06
1457∆atlE   Protein processing in endoplasmic reticulum 2.0787E-05
1457    TNF signaling pathway   2.6941E-05
1457-M10    TNF signaling pathway   4.5734E-06
1457∆atlE   TNF signaling pathway   3.3099E-06
1457    Legionellosis   0.0062434
1457-M10    Legionellosis   4.6253E-06
1457∆atlE   Legionellosis   0.0073192
1457    Epstein-Barr virus infection    0.0062434
1457-M10    Epstein-Barr virus infection    1.6635E-06
1457∆atlE   Epstein-Barr virus infection    0.00049454
1457    Toxoplasmosis   0.0064469
1457    Osteoclast differentiation  4.6509E-06
1457-M10    Osteoclast differentiation  2.6616E-05
1457    Proteasome  1.0391E-05
1457    Influenza A 1.4677E-05
1457    Herpes simplex infection    1.5915E-05
1457∆atlE   Herpes simplex infection    1.857E-06
1457    HIF-1 signaling pathway 1.6873E-05
1457-M10    NOD-like receptor signaling pathway 2.22E-06
1457∆atlE   NOD-like receptor signaling pathway 0.0096378
1457-M10    Apoptosis   9.54E-06
1457-M10    C-type lectin receptor signaling pathway    1.37E-05
1457-M10    MAPK signaling pathway  5.3439E-05
1457-M10    Endocytosis 5.49E-05
1457∆atlE   Endocytosis 1.857E-06
1457∆atlE   Neurotrophin signaling pathway  0.00049454
1457∆atlE   Ubiquitin mediated proteolysis  0.0088734
1457∆atlE   Pancreatic cancer   1.857E-06