Description Usage Arguments Examples
color_code_node_2 plot state transition network in which nodes i.e. landmarks are color-coded by average expression of the given gene
1 2 | color_code_node_2(networkFile, rpkmFile, lmFile, geneName, baseName = NULL,
seed = NULL)
|
networkFile |
a tab delimited file containing a matrix of trimmed state transition network, column and row names are landmarks, the values are 0 or 1 indicating whether the two landmarks are connected. |
rpkmFile |
a tab delimited txt file of expression data, containing cells in columns and genes in rows |
lmFile |
a tab delimited file of landmark cluster assignment of individual cells. The first column indicates cell ID, the second column indicates the landmark cluster which the cell was assigned to. |
geneName |
gene name or a vector of gene names |
baseName |
prefix name of resulting files |
seed |
the seed |
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## Not run:
rpkmFile="TPM_GSE60783_noOutlier.txt";
lmFile="TPM_GSE60783_noOutlier_geneQC0.05anyGroup_CD4vsCD8DEG_landmark_cluster.txt";
network="TPM_GSE60783_noOutlier_geneQC0.05anyGroup_CD4vsCD8DEG_state_transition_mst.txt";
# network can be the return value of trim_net
color_code_node_2(networkFile=network,
rpkmFile=rpkmFile,
lmFile=lmFile,
geneName=c("Irf8","Id2","Batf3"),
baseName="cDC1_marker",
seed=NULL)
## End(Not run)
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