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



Comments

Popular posts from this blog

Spring Elasticsearch Operations

Object oriented programming concepts (OOPs)

Network Error and Timeout on Authorize.net JS