ggplot publication quality with geom_bar and cairo

Question

I would like to make publication grade file using ggplot. I am using cairo-png but still i get some unexpected horizontal line and "black spot" on the edge of some bar.

Here the code I use:

structure(list(Sample.Name = structure(c(1L, 2L, 3L, 4L, 5L, 
6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 
19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 
32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 
45L, 46L, 47L, 48L, 49L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 
59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 68L, 69L, 70L, 71L, 
72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L, 80L, 81L, 82L, 83L, 84L, 
85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L, 93L, 94L, 95L, 96L, 97L, 
98L, 99L, 100L, 101L), .Label = c("1075", "1104", "1108", "1120", 
"1121", "1137", "1258", "1264", "1280", "1286", "1310", "1317", 
"1338", "1392", "1401", "1435", "1477", "1480", "1494", "1519", 
"1574", "1588", "1595", "1607", "1611", "1644", "1645", "1651", 
"1653", "1654", "1673", "1687", "1702", "1714", "1740", "1776", 
"1781", "1812", "1835", "1838", "1857", "1874", "1890", "1899", 
"1911", "1933", "1936", "1999", "2006", "2046", "2063", "2079", 
"2081", "2088", "2116", "2135", "2144", "2147", "2155", "2166", 
"2167", "2176", "2183", "2200", "2209", "2223", "2253", "2256", 
"2442", "2444", "2453", "2456", "2462", "2467", "2472", "2482", 
"2497", "2504", "2507", "2513", "2518", "2523", "2567", "2568", 
"2576", "2578", "2598", "2600", "2619", "2623", "2625", "2632", 
"2636", "2646", "2652", "2659", "2660", "2676", "2680", "2682", 
"2705", "2711", "2756", "2765", "2772", "2793", "2803", "2854", 
"2856", "2882", "2912", "2916", "2919", "3058", "3063", "3114", 
"3116", "3117", "3125", "3132", "3140", "3145", "3175", "3181", 
"3248", "3383", "3431", "3436", "3442", "3472", "3576", "3639", 
"4093", "FL001-1", "FL002-1", "FL004-1", "FL006-1", "FL007-1", 
"FL008-1", "FL009-1", "FL010-1", "FL017-1", "FL019-1", "FL021-1", 
"FL022-1", "FL024-1", "FL027-1", "FL028-1", "FL029-1", "FL030-1", 
"FL032-1", "FL033-1", "FL034-1", "FL035-1", "FL036-1", "FL037-1", 
"FL038-1", "FL039-1", "FL040-1", "FL041-1", "FL042-1", "FL043-1", 
"FL045-1", "FL046-1", "FL047-1", "FL049-1", "FL050-2", "FL051-1", 
"FL052-1", "FL053-1", "FL056-1", "FL057-1", "FL059-1", "FL060-1", 
"FL061-1", "FL062-1", "FL063-1", "FL064-1", "FL065-1", "FL066-1", 
"FL067-1", "FL068-1", "FL069-1", "FL071-1", "FL072-1", "FL073-1", 
"FL075-1", "FL076-1", "FL077-1", "FL078-1", "FL080-1", "FL082-1", 
"FL083-1", "FL085-1", "FL086-1", "FL087-1", "FL088-1", "FL089-1", 
"FL090-1", "FL092-1", "FL094-1", "FL095-1", "FL096-1", "FL097-1", 
"FL098-1", "FL099-1", "FL1_1215", "FL10_01501", "FL100-1", "FL101-1", 
"FL102-1", "FL103-1", "FL105-1", "FL106-1", "FL107-1", "FL110-1", 
"FL111-1", "FL112-1", "FL114-1", "FL115-1", "FL116-1", "FL117-1", 
"FL118-1", "FL119-1", "FL12_1593", "FL120-1", "FL121-1", "FL122-1", 
"FL123-1", "FL126-1", "FL127-1", "FL129-1", "FL13_01598", "FL130-1", 
"FL132-1", "FL133-1", "FL134-1", "FL135-1", "FL136-1", "FL137-1", 
"FL138-1", "FL139-1", "FL140-1", "FL141-1", "FL144-1", "FL145-1", 
"FL146-1", "FL147-1", "FL148-1", "FL149-1", "FL150-1", "FL151-1", 
"FL152-1", "FL153-1", "FL154-1", "FL156-1", "FL158-1", "FL159-1", 
"FL16_1738", "FL167-1", "FL168-1", "FL169-1", "FL17_01752", "FL170-1", 
"FL173-1", "FL176-1", "FL18_1763", "FL180-1", "FL181-1", "FL183-1", 
"FL184-1", "FL185-1", "FL187-1", "FL19_1881", "FL190-1", "FL191-1", 
"FL192-1", "FL193-1", "FL194-1", "FL195-1", "FL196-1", "FL197-1", 
"FL198-1", "FL199-1", "FL2_1222", "FL200-1", "FL22_2025", "FL23_2032", 
"FL24_02085", "FL25_2175", "FL26_2219", "FL27_02242", "FL28_2459", 
"FL3_01235", "FL30_2558", "FL35_02726", "FL37_2808", "FL41_2865", 
"FL43_02926", "FL44_2994", "FL45_3018", "FL47_3119", "FL48_3128", 
"FL55_03303", "FL62_3406", "FL64_3418", "FL65_03421", "FL69_03484", 
"FL7_1306", "FL70_03517", "FL71_03534", "FL76_3644", "FL77_3651", 
"FL8_01425"), class = "factor"), variable = structure(c(7L, 7L, 
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 
7L, 7L), .Label = c("BCL2_Status", "MLL2", "CREBBP", "TNFRSF14", 
"EZH2", "MEF2B", "ARID1A", "EP300", "IRF8", "STAT6", "CARD11", 
"GNA13", "ARID1B", "PIM1", "BCL7A", "SMARCA4", "CTSS", "TNFAIP3", 
"CCND3", "TP53", "BTG1", "FOXO1", "IKZF3", "CD79B", "DTX1", "KLHL6", 
"B2M", "P2RY8", "SGK1", "FAT2", "CIITA", "CXCR4", "ETS1", "FAS", 
"ROS1", "BTG2", "CD79A", "PAX5", "SIN3A", "TET2", "ATM", "NOTCH1", 
"NOTCH2", "UBR5", "NF1", "PIK3CD", "ARID2", "DNMT3A", "KDM6A", 
"MCL1", "SBF1", "GNB1", "IRF4", "TYK2", "ASXL1", "BRWD3", "CD40", 
"CHD2", "EPHA7", "IKZF1", "KAT2B", "BRAF", "CD58", "EPHA6", "FBXO11", 
"MALT1", "MYC", "MYD88", "PDGFRA", "RB1", "RHOA", "SMARCA2", 
"SMARCB1", "CCND1", "CDK6", "GNB2", "IKBKE", "KAT2A", "MUM1", 
"PIK3CA", "RET", "SWAP70", "TRAF6", "USP6", "ARID3A", "BIRC3", 
"CDK4", "CDKN2B", "DIRAS3", "FCGR3A", "IDH1", "IKZF2", "KAT5", 
"MDM2", "PDGFRB", "PTEN", "SF3B1", "TRAF2", "TRAF3"), class = "factor"), 
    value = c(0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 
    0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 
    0L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 
    0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 
    0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 
    0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 
    0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L)), .Names = c("Sample.Name", 
"variable", "value"), row.names = c(NA, 100L), class = "data.frame")

.

qb3r <- qplot(factor(variable),value, data = na.omit(df)) + 
  geom_bar(stat = "identity") + 
  theme(axis.text.x=element_text(angle=-90, hjust = 1), 
        text = element_text(size=8), panel.background = element_blank()) + 
  labs(title = Title_plot, x = "Gene symbol", y = "Mutated case")

ggsave("frequency FL.Ontogeny.baitset.png", type = "cairo-png", dpi= 150)

Here some example of the problem.

How could i fix it?

Thanks!

Answer 1

I think that you have two problems: using qplot instead of ggplot and not entering your x and y variables as aesthetics. ggplot2 treats x and y variables as aesthetic mappings between the data and the plot, and that mapping almost always needs to be passed via aes() or aes_string().

Here is some minimally-working code that removes the artifacts:

df <- data.frame(variable = c("Alpha","Beta","Gamma","Delta","Epsilon","Zeta"), value = runif(6))
Title_plot <- c("Some Title")
qb3r <- ggplot(aes(x = factor(variable), y = value), data = na.omit(df)) + 
  geom_bar(stat="identity") + 
  theme(axis.text.x=element_text(angle=-90, hjust = 1), 
        text = element_text(size=8), 
        panel.background = element_blank()) + 
  scale_x_discrete() +
  scale_y_continuous() +
  labs(title = Title_plot, x = "Gene symbol", y = "Mutated case")
ggsave(plot=qb3r, filename="barplottest_cairo.png", type = "cairo-png", dpi= 150)