ojooseong
commented
3 years ago Hello,
Thank you for your attention to our research.
I think the first line (column names) of your input file is not commented out. We commented out the first line (column names) of the file and did not read it from the path_table, and renamed the columns name with the command "colnames(path_table) <- c("Tara1", "Tara2", "Tara3")". If you don't want this, read the file with "path_table <- read.table(“Func_profiles/PS1Tara pathabundances.joined_cpm.R.tsv", header = TRUE, sep ='\t', quote ='')" , and then try drawing a heatmap.
I attached an example of an input file.
감사합니다. 오주성 올림
Jooseong Oh
Ph.D. Student (2016- ) Lab of Computational Systems Biology(CSB) School of Biological Sciences and Biotechnology Chonnam National University Cell: +82 10-2582-2421 Lab website: http://www.compsysbio.re.kr E-mail: ojooseong@gmail.com, ohjoosung@naver.com
2020년 12월 19일 (토) 오후 11:18, mars188 notifications@github.com님이 작성:
Hello,
I am stuck at generating a heatmap for the KEGG pathway analysis. All the above steps went well (i think) but when I run the following command in R:
d3heatmap::d3heatmap(path_table, show_grid = T,colors = "Blues", yaxis_width = 500, yaxis_font_size = 10, k_row = 5)
I get the following error: Error in rowMeans(x, na.rm = na.rm) : 'x' must be numeric
My path_table looks like this: pathway CBM_B3 CBM_D2 CBM_E2 EM1_F3 EM2_C1 EM2_G3 EM3_A5 MS1_1 MS1_2 MS1_3 OL_F4 1CMET2-PWY: N10-formyl-tetrahydrofolate biosynthesis 387.71000 332.630000 183.11900 415.31700 258.47900 50.91740 20.63740 345.013000 24.52210 254.026000 114.10800 . . . Like the first column contains the name of the pathway and the rest of the columns are sample names...
Can anyone please help me to find out why I am getting the above error? and not generating the KEGG heatmap.
Many thanks,
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Hello,
I am stuck at generating a heatmap for the KEGG pathway analysis. All the above steps went well (i think) but when I run the following command in R:
d3heatmap::d3heatmap(path_table, show_grid = T,colors = "Blues", yaxis_width = 500, yaxis_font_size = 10, k_row = 5)
I get the following error: Error in rowMeans(x, na.rm = na.rm) : 'x' must be numeric
My path_table looks like this: pathway CBM_B3 CBM_D2 CBM_E2 EM1_F3 EM2_C1 EM2_G3 EM3_A5 MS1_1 MS1_2 MS1_3 OL_F4 1CMET2-PWY: N10-formyl-tetrahydrofolate biosynthesis 387.71000 332.630000 183.11900 415.31700 258.47900 50.91740 20.63740 345.013000 24.52210 254.026000 114.10800 . . . Like the first column contains the name of the pathway and the rest of the columns are sample names...
Can anyone please help me to find out why I am getting the above error? and not generating the KEGG heatmap.
Many thanks,