Unable to display minor grid lines in ggplot2
I am trying to differentiate the tiles by displaying white minor grid lines but I am unable to get it to work. Could someone help me please.
This is what my function looks like. I have tried changing the panel.grid.minor to specify x & y gridlines as well. Didnt work. Help please. Thanks in advance
library(ggplot2)
library(tidyverse)
# Read the data
data <- read.table("pd_output.txt", header = TRUE, sep = "\t")
# Create a generic waterfall plot function
create_waterfall_plot <- function(data) {
data <- data %>%
mutate(mutation_types = factor(mutation_types),
variant_consequences = factor(variant_consequences),
impact = factor(impact),
clinical_annotations = factor(clinical_annotations),
TE_fusion = factor(TE_fusion),
hotspot = factor(hotspot))
plot <- ggplot(data, aes(x = sampleID, y = gene_name)) +
theme_bw() +
theme(panel.grid.major = element_blank(),
panel.grid.minor = element_line(size = 2, colour ="white"),
axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
geom_tile(aes(fill = variant_consequences, colour = mutation_types, alpha = 0.5), size = 0.5, width = 0.8, height = 0.8) +
geom_point(aes(shape = mutation_types, colour = impact), size = 3) +
scale_fill_manual(values = c("missense_variant" = "blue", "splice_donor_variant" = "orange", "stop_gained" = "darkgreen", "frameshift_variant" = "yellow", "inframe_deletion" = "brown", "missense_variant&splice_region_variant" = "violet", "stop_gained & inframe_deletion" = "gray", "inframe_insertion" = "cyan")) +
scale_color_manual(values = c("MODERATE" = "lightpink", "HIGH" = "red")) +
labs(x = "Sample ID", y = "Gene Name",
fill = "Variant Consequences", colour = "Impact", shape = "CLONALITY") +
guides(alpha = FALSE)
return(plot)
}
# Generate the waterfall plot
waterfall_plot <- create_waterfall_plot(data)
print(waterfall_plot)
Sample data looks like this
sampleID gene_name mutation_types variant_consequences impact clinical_annotations TE_fusion hotspot
P-0028 NCOR1 CLONAL missense_variant MODERATE localised no no
P-0029 SETD2 CLONAL splice_donor_variant HIGH localised yes yes
P-0030 ATM SUBCLONAL stop_gained HIGH localised no no
P-0031 CDKN1B CLONAL frameshift_variant HIGH localised yes no
P-0032 KMT2C CLONAL stop_gained HIGH metastatic no no
P-0033 FOXA1 CLONAL stop_gained HIGH metastatic yes yes
P-0034 NCOR1 CLONAL missense_variant MODERATE metastatic yes no
P-0035 KMT2A CLONAL missense_variant MODERATE localised yes no
P-0036 KMT2C CLONAL missense_variant MODERATE localised yes no
current output plot looks like this
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