Hi,
I would like to use custom colors instead of default colors in dba.plotHeatmap. The below is my command lines and error messages, could you help me to trouble shooting? Many thanks.
Best,
Gary
> atac <- dba(sampleSheet = "atac.csv",peakFormat = "bed")
CTNNB1_G8_13 13 CTNNB1 RCAS Treat 1 MACS2
CTNNB1_G8_14 14 CTNNB1 RCAS Treat 2 MACS2
CTNNB1_G8_15 15 CTNNB1 RCAS Treat 3 MACS2
GFP_G7_1 1 GFP Control Control 1 MACS2
GFP_G7_2 2 GFP Control Control 2 MACS2
GFP_G7_3 3 GFP Control Control 3 MACS2
RA_G7_7 7 RA RA Treat 1 MACS2
RA_G7_8 8 RA RA Treat 2 MACS2
RA_G7_9 9 RA RA Treat 3 MACS2
Sox2_G7_4 4 Sox2 RCAS Treat 1 MACS2
Sox2_G7_5 5 Sox2 RCAS Treat 2 MACS2
Sox2_G7_6 6 Sox2 RCAS Treat 3 MACS2
Spry2_G7_17 17 Spry2 RCAS Treat 2 MACS2
Spry2_G7_18 18 Spry2 RCAS Treat 3 MACS2
> atac
14 Samples, 49591 sites in matrix (64933 total):
ID Tissue Factor Condition Treatment Replicate Caller Intervals
1 CTNNB1_G8_13 13 CTNNB1 RCAS Treat 1 MACS2 12531
2 CTNNB1_G8_14 14 CTNNB1 RCAS Treat 2 MACS2 16577
3 CTNNB1_G8_15 15 CTNNB1 RCAS Treat 3 MACS2 7428
4 GFP_G7_1 1 GFP Control Control 1 MACS2 39995
5 GFP_G7_2 2 GFP Control Control 2 MACS2 45248
6 GFP_G7_3 3 GFP Control Control 3 MACS2 40385
7 RA_G7_7 7 RA RA Treat 1 MACS2 29027
8 RA_G7_8 8 RA RA Treat 2 MACS2 12608
9 RA_G7_9 9 RA RA Treat 3 MACS2 27233
10 Sox2_G7_4 4 Sox2 RCAS Treat 1 MACS2 43518
11 Sox2_G7_5 5 Sox2 RCAS Treat 2 MACS2 37854
12 Sox2_G7_6 6 Sox2 RCAS Treat 3 MACS2 44068
13 Spry2_G7_17 17 Spry2 RCAS Treat 2 MACS2 25495
14 Spry2_G7_18 18 Spry2 RCAS Treat 3 MACS2 26104
> dba.plotHeatmap(atac,ColAttributes = DBA_FACTOR)
> dba.plotHeatmap(atac,ColAttributes = DBA_FACTOR, colSideCols = c(mediumpurple1, mediumpurple1, mediumpurple1, palegreen2, palegreen2, palegreen2, lightskyblue, lightskyblue, lightskyblue, orange, orange, orange, orchid1, orchid1, orchid1))
Error: object 'mediumpurple1' not found
In addition: Warning messages:
1: display list redraw incomplete
2: display list redraw incomplete
Thank you so much for you quickly response. The correct command is below. Another problem of my original command is that there are too many colors.
> dba.plotHeatmap(atac,ColAttributes = DBA_FACTOR, colSideCols = c("mediumpurple1", "palegreen2", "lightskyblue", "orange", "orchid1"))